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El Fadili M, Er-Rajy M, Ali Eltayb W, Kara M, Imtara H, Zarougui S, Al-Hoshani N, Hamadi A, Elhallaoui M. An in-silico investigation based on molecular simulations of novel and potential brain-penetrant GluN2B NMDA receptor antagonists as anti-stroke therapeutic agents. J Biomol Struct Dyn 2024; 42:6174-6188. [PMID: 37428078 DOI: 10.1080/07391102.2023.2232024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
GluN2B-induced activation of NMDA receptors plays a key function in central nervous system (CNS) disorders, including Parkinson, Alzheimer, and stroke, as it is strongly involved in excitotoxicity, which makes selective NMDA receptor antagonists one of the potential therapeutic agents for the treatment of neurodegenerative diseases, especially stroke. The present study aims to examine a structural family of thirty brain-penetrating GluN2B N-methyl-D-aspartate (NMDA) receptor antagonists, using virtual computer-assisted drug design (CADD) to discover highly candidate drugs for ischemic strokes. Initially, the physicochemical and ADMET pharmacokinetic properties confirmed that C13 and C22 compounds were predicted as non-toxic inhibitors of CYP2D6 and CYP3A4 cytochromes, with human intestinal absorption (HIA) exceeding 90%, and designed to be as efficient central nervous system (CNS) agents due to the highest probability to cross the blood-brain barrier (BBB). Compared to ifenprodil, a co-crystallized ligand complexed with the transport protein encoded as 3QEL.pdb, we have noticed that C13 and C22 chemical compounds were defined by good ADME-Toxicity profiles, meeting Lipinski, Veber, Egan, Ghose, and Muegge rules. The molecular docking results indicated that C22 and C13 ligands react specifically with the amino acid residues of the NMDA receptor subunit GluN1 and GluN2B. These intermolecular interactions produced between the candidate drugs and the targeted protein in the B chain remain stable over 200 nanoseconds of molecular dynamics simulation time. In conclusion, C22 and C13 ligands are highly recommended as anti-stroke therapeutic drugs due to their safety and molecular stability towards NMDA receptors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed El Fadili
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Mohammed Er-Rajy
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Wafa Ali Eltayb
- Biotechnology Department, Faculty of Sciences and Technology, Shendi University, Shendi, Sudan
| | - Mohammed Kara
- Laboratory of Biotechnology, Conservation and Valorisation of Naturals Resources, Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hamada Imtara
- Faculty of Arts and Sciences, Arab American University Palestine, Jenin, Palestine
| | - Sara Zarougui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Nawal Al-Hoshani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abdullah Hamadi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Menana Elhallaoui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
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2
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Sravanthi B, Himavathi G, Robert AR, Karunakar P, Kiran KS, Maddila S. Design, synthesis, computational molecular docking studies of novel heterocyclics bearing 1,2,4-triazole, 1,3,4-oxadiazole conjugates as potent antibacterial and antitubercular agents. J Biomol Struct Dyn 2024; 42:5376-5389. [PMID: 37340639 DOI: 10.1080/07391102.2023.2226743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 06/11/2023] [Indexed: 06/22/2023]
Abstract
Herein, we report the synthesis, and characterization of a new series of 1,3,4-oxadiazole and 1,2,4-triazole derivatives based on azaindole acetamides and assigned as potential antibacterial and antitubercular substances. The structures of these compounds were established by 1H NMR, 13C NMR, and HRMS spectral analysis. In preliminary antibacterial studies, analogues 6b, 6d, and 6e were found to be most effective against S. aureus with MIC of 12.5, 6.25, and 12.5 μg/mL, whereas 8d displayed excellent activity against S. aureus, B. subtilis, E. coli bacterial strains with zones of inhibition 12.5, 25, and 12.5 μg/mL respectively. Particularly, the prepared scaffolds 8c, 8d, and 8e showed remarkable antifungal activity with MIC value 12.5, 12.5, and 6.25 μg/mL against A. flavus and 6d, 6c producing an increase in the activity against C. Albicans with zones of inhibition 12.5 and 12.5 μg/mL respectively. Also, through the antitubercular studies, we found that compounds 6e and 8b have a strong activity with M. tuberculosis H37Rv with MICs 3.26, and 6.48 μg/mL, respectively. The protein stability, fluctuations of APO-Protein, and protein-ligand complexes were investigated through Molecular Dynamics (MD) simulations studies using Desmond Maestro 11.3, and potential lead molecules were identified. Our findings were further confirmed using molecular docking, revealing that azaindole based ligand 6e, 6f, and 8a has strong hydrophobic Tyr179, Trp183, Ile177, Ile445, and H-bondings interactions Arg151 and Arg454 through molecular dynamics simulation studies, making it potential biological compound. These compounds were further evaluated for their ADMET and physicochemical properties by using SwissADME.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B Sravanthi
- Department of Chemistry, GITAM School of Sciences, GITAM University, Visakhapatnam, India
- Department of Chemistry, Institute of Aeronautical Engineering, Hyderabad, India
| | - G Himavathi
- Department of Chemistry, GITAM School of Sciences, GITAM University, Visakhapatnam, India
| | - A R Robert
- Department of Chemistry, GITAM School of Sciences, GITAM University, Visakhapatnam, India
| | - Prashantha Karunakar
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvarava Technological University), Bangalore, India
| | - K S Kiran
- Department of Physics, Faculty of Engineering and Technology, Jain University, Bangalore, India
| | - S Maddila
- Department of Chemistry, GITAM School of Sciences, GITAM University, Visakhapatnam, India
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
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Nemr MTM, Elshewy A, Ibrahim ML, El Kerdawy AM, Halim PA. Design, synthesis, antineoplastic activity of new pyrazolo[3,4-d]pyrimidine derivatives as dual CDK2/GSK3β kinase inhibitors; molecular docking study, and ADME prediction. Bioorg Chem 2024; 150:107566. [PMID: 38896936 DOI: 10.1016/j.bioorg.2024.107566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/06/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024]
Abstract
In the current study, novel pyrazolo[3,4-d]pyrimidine derivatives 5a-h were designed and synthesized as targeted anti-cancer agents through dual CDK2/GSK-3β inhibition. The designed compounds demonstrated moderate to potent activity on the evaluated cancer cell lines (MCF-7 and T-47D). Compounds 5c and 5 g showed the most promising cytotoxic activity against the tested cell lines surpassing that of the used reference standard; staurosporine. On the other hand, both compounds showed good safety and tolerability on normal fibroblast cell line (MCR5). The final compounds 5c and 5 g showed a promising dual CDK2/GSK-3β inhibitory activity with IC50 of 0.244 and 0.128 μM, respectively, against CDK2, and IC50 of 0.317 and 0.160 μM, respectively, against GSK-3β. Investigating the effect of compounds 5c and 5 g on CDK2 and GSK-3β downstream cascades showed that they reduced the relative cellular content of phosphorylated RB1 and β-catenin compared to that in the untreated MCF-7 cells. Moreover, compounds 5c and 5 g showed a reasonable selective inhibition against the target kinases CDK2/GSK-3β in comparison to a set of seven off-target kinases. Furthermore, the most potent compound 5 g caused cell cycle arrest at the S phase in MCF-7 cells preventing the cells' progression to G2/M phase inducing cell apoptosis. Molecular docking studies showed that the final pyrazolo[3,4-d]pyrimidine derivatives have analogous binding modes in the target kinases interacting with the hinge region key amino acids. Molecular dynamics simulations confirmed the predicted binding mode by molecular docking. Moreover, in silico predictions indicated their favorable physicochemical and pharmacokinetic properties in addition to their promising cytotoxic activity.
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Affiliation(s)
- Mohamed T M Nemr
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Ahmed Elshewy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt; Department of Medicinal Chemistry, Faculty of Pharmacy, Galala University, New Galala 43713, Egypt.
| | - Mohammed L Ibrahim
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Ahmed M El Kerdawy
- School of Pharmacy, College of Health and Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, United Kingdom; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Peter A Halim
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
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Bondock S, Alabbad N, Hossan A, Abdou MM, Shati AA, Alfaifi MY, Elbehairi SEI, Mohamed NM. Design, synthesis, and anticancer evaluation of novel coumarin/thiazole congeners as potential CDK2 inhibitors with molecular dynamics. RSC Adv 2024; 14:18838-18855. [PMID: 38873551 PMCID: PMC11167341 DOI: 10.1039/d4ra02456g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/28/2024] [Indexed: 06/15/2024] Open
Abstract
A series of novel coumarin-thiazoles was designed and synthesized as a possible CDK2 inhibitor with anticancer activity with low toxicity. The design relied on having hydrazine thiazole or its open-form thioamide to form H-bonds with the ATP binding site while coumarin maintained the crucial hydrophobic interactions for proper fitting. The biological evaluation revealed that the hydroxycoumarin-thiazole derivative 6c demonstrated the best inhibition with HepG2 and HCT116 IC50 2.6 and 3.5 μM, respectively. Similarly, its open thioamide chain congener 5c exhibited potent inhibition on MCF-7 and HepG2 with IC50 of 4.5 and 5.4 μM, respectively. Molecular docking simulations supported the assumption of inhibiting CDK2 by preserving the crucial interaction pattern with the hinge ATP site and the surrounding hydrophobic (HPO) side chains. Furthermore, molecular dynamics simulations of 5c and 6c established satisfactory stability and affinity within the CDK2 active site.
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Affiliation(s)
- Samir Bondock
- Chemistry Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Nada Alabbad
- Chemistry Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Aisha Hossan
- Chemistry Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Moaz M Abdou
- Egyptian Petroleum Research Institute Nasr City 11727 Cairo Egypt
| | - Ali A Shati
- Biology Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Mohammad Y Alfaifi
- Biology Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Serag E I Elbehairi
- Biology Department, Faculty of Science, King Khalid University 9004 Abha Saudi Arabia
| | - Nada M Mohamed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information, MTI Cairo Egypt
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5
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Lin J, Bu G, Unge J, Gonen T. An Updated Structure of Oxybutynin Hydrochloride. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597682. [PMID: 38895300 PMCID: PMC11185708 DOI: 10.1101/2024.06.05.597682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Oxybutynin (Ditropan), a widely distributed muscarinic antagonist for treating the overactive bladder, has been awaiting a definitive crystal structure for nearly 50 years due to the sample and technique limitations. Past reports used powder X-ray diffraction (PCRD) to shed light on the possible packing of the molecule however a 3D structure remained elusive. Here we used Microcrystal Electron Diffraction (MicroED) to successfully unveil the 3D structure of oxybutynin hydrochloride. We identify several inconsistencies between the reported PXRD analyses and the experimental structure. Using the improved model, molecular docking was applied to investigate the binding mechanism between M3 muscarinic receptor (M3R) and (R)-oxybutynin, revealing essential contacts/residues and conformational changes within the protein pocket. A possible universal conformation was proposed for M3R antagonists, which is valuable for future drug development and optimization. This study underscores the immense potential of MicroED as a complementary technique for elucidating the unknown pharmaceutical crystal structures, as well as for the protein-drug interactions.
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Affiliation(s)
- Jieye Lin
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Guanhong Bu
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Johan Unge
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Department of Physiology, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
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6
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Sangsuwan W, Taweesablamlert A, Boonkerd A, Isarangkool Na Ayutthaya C, Yoo S, Javid B, Faikhruea K, Vilaivan T, Aonbangkhen C, Chuawong P. A quest for novel antimicrobial targets: Inhibition of Asp-tRNA Asn/Glu-tRNA Gln amidotransferase (GatCAB) by synthetic analogs of aminoacyl-adenosine in vitro and live bacteria. Bioorg Chem 2024; 150:107530. [PMID: 38852310 DOI: 10.1016/j.bioorg.2024.107530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
The Asp-tRNAAsn/Glu-tRNAGln amidotransferase (GatCAB) has been proposed as a novel antibacterial drug target due to its indispensability in prominent human pathogens. While several inhibitors with in vitro activity have been identified, none have been demonstrated to have potent activity against live bacteria. In this work, seven non-hydrolyzable transition state mimics of GatCAB were synthesized and tested as the transamidase inhibitors against GatCAB from the human pathogen Helicobacter pylori. Notably, the methyl sulfone analog of glutamyl-adenosine significantly reduced GatCAB's transamination rate. Additionally, four lipid-conjugates of these mimics displayed antibacterial activity against Bacillus subtilis, likely due to enhanced cell permeability. Inhibitory activity against GatCAB in live bacteria was confirmed using a sensitive gain-of-function dual luciferase reporter in Mycobacterium bovis-BCG. Only the lipid-conjugated methyl sulfone analog exhibited a significant increase in mistranslation rate, highlighting its cell permeability and inhibitory potential. This study provides insights for developing urgently needed novel antibacterial agents amidst emerging antimicrobial drug resistance.
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Affiliation(s)
- Withsakorn Sangsuwan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Amata Taweesablamlert
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Anon Boonkerd
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Chawarat Isarangkool Na Ayutthaya
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Sion Yoo
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Babak Javid
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Kriangsak Faikhruea
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand; Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Pitak Chuawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand.
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Zaib S, Khan I, Ali HS, Younas MT, Ibrar A, Al-Odayni AB, Al-Kahtani AA. Design and discovery of anthranilamide derivatives as a potential treatment for neurodegenerative disorders via targeting cholinesterases and monoamine oxidases. Int J Biol Macromol 2024; 272:132748. [PMID: 38821306 DOI: 10.1016/j.ijbiomac.2024.132748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Neurodegenerative diseases with progressive cellular loss of the central nervous system and elusive disease etiology provide a continuous impetus to explore drug discovery programmes aiming at identifying robust and effective inhibitors of cholinesterase and monoamine oxidase enzymes. We herein present a concise library of anthranilamide derivatives involving a palladium-catalyzed Suzuki-Miyaura cross-coupling reaction to install the diverse structural diversity required for the desired biological action. Using Ellman's method, cholinesterase inhibitory activity was performed against AChE and BuChE enzymes. In vitro assay results demonstrated that anthranilamides are potent inhibitors with remarkable potency. Compound 6k emerged as the lead candidate and dual inhibitor of both enzymes with IC50 values of 0.12 ± 0.01 and 0.49 ± 0.02 μM against AChE and BuChE, respectively. Several other compounds were found as highly potent and selective inhibitors. Anthranilamide derivatives were also tested against monoamine oxidase (A and B) enzymes using fluorometric method. In vitro data revealed compound 6h as the most potent inhibitor against MAO-A, showing an IC50 value of 0.44 ± 0.02 μM, whereas, compound 6k emerged as the top inhibitor of MAO-B with an IC50 value of 0.06 ± 0.01 μM. All the lead inhibitors were analyzed for the identification of their mechanism of action using Michaelis-Menten kinetics experiments. Compound 6k and 6h depicted a competitive mode of action against AChE and MAO-A, whereas, a non-competitive and mixed-type of inhibition was observed against BuChE and MAO-B by compounds 6k. Molecular docking analysis revealed remarkable binding affinities of the potent inhibitors with specific residues inside the active site of receptors. Furthermore, molecular dynamics simulations were performed to explore the ability of potent compounds to form energetically stable complexes with the target protein. Finally, in silico ADME calculations also demonstrated that the potent compounds exhibit promising pharmacokinetic profile, satisfying the essential criteria for drug-likeness. Altogether, the findings reported in the current work clearly suggest that the identified anthranilamide derivatives have the potential to serve as effective drug candidates for future investigations.
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Affiliation(s)
- Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan.
| | - Imtiaz Khan
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester MI 7DN, UK.
| | - Hafiz Saqib Ali
- Chemistry Research Laboratory, Department of Chemistry, the INEOS Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Muhammad Tayyab Younas
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Aliya Ibrar
- Department of Chemistry, Faculty of Physical and Applied Sciences, The University of Haripur, Haripur, KPK 22620, Pakistan.
| | - Abdel-Basit Al-Odayni
- Department of Restorative Dental Sciences, College of Dentistry, King Saud University, P.O. Box 60169, Riyadh 11545, Saudi Arabia
| | - Abdullah A Al-Kahtani
- Chemistry Department, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
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Cyboran-Mikołajczyk S, Matczak K, Olchowik-Grabarek E, Sękowski S, Nowicka P, Krawczyk-Łebek A, Kostrzewa-Susłow E. The influence of the chlorine atom on the biological activity of 2'-hydroxychalcone in relation to the lipid phase of biological membranes - Anticancer and antimicrobial activity. Chem Biol Interact 2024; 398:111082. [PMID: 38825055 DOI: 10.1016/j.cbi.2024.111082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
The study investigates the effect of the presence of a chlorine atom in the 2'-hydroxychalcone molecule on its interaction with model lipid membranes, in order to discern its potential pharmacological activity. Five chlorine derivatives of 2'-hydroxychalcone were synthesized and evaluated against liposomes composed of POPC and enriched with cationic (DOTAP) or anionic (POPG) lipids. The physicochemical properties of the compounds were initially simulated using SwissAdame software, revealing high lipophilicity (ilogP values: 2.79-2.90). The dynamic light scattering analysis of liposomes showed that chloro chalcones induce minor changes in the diameter of liposomes of different surface charges. Fluorescence quenching assays with a TMA-DPH probe demonstrated the strong ability of the compounds to interact with the lipid bilayer, with varying quenching capacities based on chlorine atom position. FTIR studies indicated alterations in carbonyl, phosphate, and choline groups, suggesting a transition area localization rather than deep penetration into the hydrocarbon chains. Additionally, dipole potential reduction was observed in POPC and POPC-POPG membranes, particularly pronounced by derivatives with a chlorine atom in the B ring. Antibacterial and antibiofilm assays revealed enhanced activity of derivatives with a chlorine atom compared to 2'-hydroxychalcone, especially against Gram-positive bacteria. The MIC and MBIC50 values showed increased efficacy in the presence of chlorine with 3'-5'-dichloro-2'-hydroxychalcone demonstrating optimal antimicrobial and antibiofilm activity. Furthermore, antiproliferative assays against breast cancer cell lines indicated higher activity of B-ring chlorine derivatives, particularly against MDA-MB-231 cells. In general, the presence of a chlorine atom in 2'-hydroxychalcone improves its pharmacological potential, with derivatives showing improved antimicrobial, antibiofilm, and antiproliferative activities, especially against aggressive breast cancer cell lines. These findings underscore the importance of molecular structure in modulating biological activity and highlight chalcones with a chlorine as promising candidates for further drug development studies.
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Affiliation(s)
- Sylwia Cyboran-Mikołajczyk
- Department of Physics and Biophysics, Wrocław University of Environmental and Life Sciences, Norwida St. 25, 50-375, Wrocław, Poland.
| | - Karolina Matczak
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St. 141/143, 90-236, Lodz, Poland
| | - Ewa Olchowik-Grabarek
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Bialystok, Konstanty Ciolkowski St. 1J, 15-245, Białystok, Poland
| | - Szymon Sękowski
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Bialystok, Konstanty Ciolkowski St. 1J, 15-245, Białystok, Poland
| | - Paulina Nowicka
- Department of Fruit, Vegetable and Plant Nutraceutical Technology, Wrocław University of Environmental and Life Sciences, Chełmońskiego St. 37, 50-375, Wrocław, Poland
| | - Agnieszka Krawczyk-Łebek
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida St. 25, 50-375, Wrocław, Poland
| | - Edyta Kostrzewa-Susłow
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida St. 25, 50-375, Wrocław, Poland
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Ramadan SK, Abd-Rabboh HSM, Abdel Hafez AA, Abou-Elmagd WSI. Some pyrimidohexahydroquinoline candidates: synthesis, DFT, cytotoxic activity evaluation, molecular docking, and in silico studies. RSC Adv 2024; 14:16584-16599. [PMID: 38779387 PMCID: PMC11109844 DOI: 10.1039/d4ra02271h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Some hexahydroquinoline candidates were prepared by reacting 2-amino-3-cyano-1-cyclohexylhexahydroquinoline with oxalyl chloride and triethyl orthoformate. The computational chemical approach agreed with the product-testing results. The produced substances were examined in vitro for their antiproliferative activity against liver carcinoma (HepG2), breast adenocarcinoma (MCF7), prostate cancer (PC3), and colon cancer (HCT116) cell lines. The highest potency against the four cell lines was exhibited by hydrazide, thiosemicarbazide, and thiazolidinone derivatives. The best docking score was presented by thiosemicarbazide and thiazolidinone derivatives as they showed the highest binding to the Mcl-1 enzyme with binding energies of -8.97 and -8.90 kcal mol-1, respectively, which were higher than that of the co-crystallized ligand (LC3) with a binding energy of -8.74 kcal mol-1. Besides, the modeling pharmacokinetics disclosed their desirable drug-likeness and oral bioavailability characteristics.
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Affiliation(s)
- Sayed K Ramadan
- Chemistry Department, Faculty of Science, Ain Shams University Cairo 11566 Egypt
| | - Hisham S M Abd-Rabboh
- Chemistry Department, College of Science, King Khalid University P. O. Box 9004 Abha 62223 Saudi Arabia
| | - Amal A Abdel Hafez
- Chemistry Department, College of Science, King Khalid University P. O. Box 9004 Abha 62223 Saudi Arabia
| | - Wael S I Abou-Elmagd
- Chemistry Department, Faculty of Science, Ain Shams University Cairo 11566 Egypt
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10
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Faris M, Bostancı HE, Özcan İ, Öztürk M, Koçyiğit ÜM, Erdoğan T, Tahtaci H. Imidazole-Derived Alkyl and Aryl Ethers: Synthesis, Characterization, In Vitro Anticancer and Antioxidant Activities, Carbonic Anhydrase I-II Inhibition Properties, and In Silico Studies. ACS OMEGA 2024; 9:20937-20956. [PMID: 38764643 PMCID: PMC11097166 DOI: 10.1021/acsomega.4c00028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/21/2024]
Abstract
Imidazole derivatives display extensive applications in pharmaceutical chemistry and have been investigated as bioactive compounds for medicinal chemistry. In this study, besides the starting materials (3a-c and 4a-c), synthesis, characterization, and biological activity studies were conducted on a total of 18 compounds, nine of which are known and the other nine are original. The compounds investigated in the study are a series of alkyl (7-15) and aryl (16-24) ether derivatives bearing substituted phenyl and imidazole rings, which were characterized using various methods including 1H NMR, 13C NMR, FT-IR analysis, elemental analysis, and mass spectroscopy. Computer-aided drug design studies have been carried out to predict the biological activities of compounds. Besides DFT calculations, the binding affinities of the compounds to EGFR, VEGFR2, FGFR1, HSP90, hCA I, and hCA II were investigated. Additionally, drug-likeness and ADME analyses were performed on the compounds. Anticancer, antioxidant, and enzyme inhibition activity tests were performed in biological activity studies on the synthesized compounds. Among the synthesized compounds, compounds 17 and 19-24 generally exhibited inhibition profiles against the widespread cytosolic hCA I isozyme with IC50 values ranging from 4.13 to 15.67 nM and cytosolic hCA II isozyme with IC50 values ranging from 5.65 to 14.84 nM. L929 (mouse fibroblast cell line) was used as the control healthy cell line, and MCF7 (breast cancer), C6 (rat glioblastoma), and HT-29 (colon cancer) cells were used in cell culture studies as cancer cell lines. Before the study on cancer cells, all compounds were examined on healthy cells, and their cytotoxicity was determined. As a result of these data, studies continued with six compounds determined to be nontoxic. On cancerous cells, it was determined that compounds 3a, 3b, 4a, 4b, 4c, and 7 had cytotoxic effects on both colon cancer and brain tumors. It was found that compound 3b had a more toxic effect than cisplatin on the glioma cell line with an IC50 value of 10.721 ± 0.38 μM, and compound 3a had a more toxic effect on the colon cancer cell line with an IC50 value of 20.88 ± 1.02 μM. However, it was determined that the same compounds did not have a statistically significant effect on breast cancer. Flow cytometry studies also showed that when the IC50 dose of compound 3b was applied to the C6 cell line, the cells tended to early and late apoptosis. Additionally, it has been shown by flow cytometry that the cell cycle stops in the G0/G1 phase. A similar effect was observed in the colon cancer cell line with compound 3a. Compound 3b caused early and late apoptosis of the colon cancer cell line with the applied IC50 dose and stopped the cell cycle in the G0/G1 phase. Finally, the FRAP method studied all synthesized compounds' antioxidant effects. According to the measured antioxidant power results, it was determined that no compound had a more effective reducing power than vitamin E.
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Affiliation(s)
- Mays Faris
- Department
of Chemistry, Faculty of Science, Karabuk
University, 78050 Karabuk, Türkiye
| | - Hayrani Eren Bostancı
- Department
of Biochemistry Sivas, Faculty of Pharmacy, Sivas Cumhuriyet University, 58010 Sivas, Türkiye
| | - İbrahim Özcan
- Department
of Chemistry, Faculty of Science, Karabuk
University, 78050 Karabuk, Türkiye
| | - Mustafa Öztürk
- Sivas
Vocational School of Technical Sciences, Sivas Cumhuriyet University, 58010 Sivas, Türkiye
| | - Ümit Muhammed Koçyiğit
- Department
of Biochemistry Sivas, Faculty of Pharmacy, Sivas Cumhuriyet University, 58010 Sivas, Türkiye
| | - Taner Erdoğan
- Kocaeli
Vocational School, Department of Chemistry and Chemical Processing
Technologies, Kocaeli University, 41140 Kocaeli, Türkiye
| | - Hakan Tahtaci
- Department
of Chemistry, Faculty of Science, Karabuk
University, 78050 Karabuk, Türkiye
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11
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Guo W, Liu Y, Chen B, Fan L. Target prediction and potential application of dihydroartemisinin on hepatocarcinoma treatment. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03123-6. [PMID: 38713259 DOI: 10.1007/s00210-024-03123-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
With high incidence of hepatocarcinoma and limited effective treatments, most patients suffer in pain. Antitumor drugs are single-targeted, toxicity, causing adverse side effects and resistance. Dihydroartemisinin (DHA) inhibits tumor through multiple mechanisms effectively. This study explores and evaluates safety and potential mechanism of DHA towards human hepatocarcinoma based on network pharmacology in a comprehensive way. Adsorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of DHA were evaluated with pkCSM, SwissADME, and ADMETlab. Potential targets of DHA were obtained from SwissTargetPrediction, Drugbank, TargetNET, and PharmMapper. Target gene of hepatocarcinoma was obtained from OMIM, GeneCards, and DisGeNET. Overlapping targets and hub genes were identified and analyzed for Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome pathway. Molecular docking was utilized to investigate the interactions sites and hydrogen bonds. Cell counting kit-8 (CCK8), wound healing, invasion, and migration assays on HepG2 and SNU387 cell proved DHA inhibits malignant biological features of hepatocarcinoma cell. DHA is safe and desirable for clinical application. A total of 131 overlapping targets were identified. Biofunction analysis showed targets were involved in kinase activity, protein phosphorylation, intracellular reception, signal transduction, transcriptome dysregulation, PPAR pathway, and JAK-STAT signaling axis. Top 9 hub genes were obtained using MCC (Maximal Clique Centrality) algorithm, namely CDK1, CCNA2, CCNB1, CCNB2, KIF11, CHEK1, TYMS, AURKA, and TOP2A. Molecular docking suggests that all hub genes form a stable interaction with DHA for optimal binding energy were all less than - 5 kcal/mol. Dihydroartemisinin might be a potent and safe anticarcinogen based on its biological safety and effective therapeutic effect.
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Affiliation(s)
- Wenjia Guo
- Department of Laboratory Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yu'e Liu
- Tongji University Cancer Center, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Bingdi Chen
- The Institute for Biomedical Engineering and Nano Science, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Lieying Fan
- Department of Laboratory Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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12
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Pele R, Marc G, Mogoșan C, Apan A, Ionuț I, Tiperciuc B, Moldovan C, Araniciu C, Oniga I, Pîrnău A, Vlase L, Oniga O. Synthesis, In Vivo Anticonvulsant Activity Evaluation and In Silico Studies of Some Quinazolin-4(3H)-One Derivatives. Molecules 2024; 29:1951. [PMID: 38731442 PMCID: PMC11085150 DOI: 10.3390/molecules29091951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Two series, "a" and "b", each consisting of nine chemical compounds, with 2,3-disubstituted quinazolin-4(3H)-one scaffold, were synthesized and evaluated for their anticonvulsant activity. They were investigated as dual potential positive allosteric modulators of the GABAA receptor at the benzodiazepine binding site and inhibitors of carbonic anhydrase II. Quinazolin-4(3H)-one derivatives were evaluated in vivo (D1-3 = 50, 100, 150 mg/kg, administered intraperitoneally) using the pentylenetetrazole (PTZ)-induced seizure model in mice, with phenobarbital and diazepam, as reference anticonvulsant agents. The in silico studies suggested the compounds act as anticonvulsants by binding on the allosteric site of GABAA receptor and not by inhibiting the carbonic anhydrase II, because the ligands-carbonic anhydrase II predicted complexes were unstable in the molecular dynamics simulations. The mechanism targeting GABAA receptor was confirmed through the in vivo flumazenil antagonism assay. The pentylenetetrazole experimental anticonvulsant model indicated that the tested compounds, 1a-9a and 1b-9b, present a potential anticonvulsant activity. The evaluation, considering the percentage of protection against PTZ, latency until the onset of the first seizure, and reduction in the number of seizures, revealed more favorable results for the "b" series, particularly for compound 8b.
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Affiliation(s)
- Raluca Pele
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (R.P.); (G.M.); (I.I.); (B.T.); (C.M.); (O.O.)
| | - Gabriel Marc
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (R.P.); (G.M.); (I.I.); (B.T.); (C.M.); (O.O.)
| | - Cristina Mogoșan
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 6A Louis Pasteur Street, 400349 Cluj-Napoca, Romania;
| | - Anamaria Apan
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 6A Louis Pasteur Street, 400349 Cluj-Napoca, Romania;
| | - Ioana Ionuț
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (R.P.); (G.M.); (I.I.); (B.T.); (C.M.); (O.O.)
| | - Brîndușa Tiperciuc
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (R.P.); (G.M.); (I.I.); (B.T.); (C.M.); (O.O.)
| | - Cristina Moldovan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (R.P.); (G.M.); (I.I.); (B.T.); (C.M.); (O.O.)
| | - Cătălin Araniciu
- Department of Therapeutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 12 Ion Creangă, 400010 Cluj-Napoca, Romania;
| | - Ilioara Oniga
- Department of Pharmacognosy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 12 Ion Creangă, 400010 Cluj-Napoca, Romania;
| | - Adrian Pîrnău
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat Street, 400293 Cluj-Napoca, Romania;
| | - Laurian Vlase
- Department of Pharmaceutical Technology and Biopharmaceutics, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (R.P.); (G.M.); (I.I.); (B.T.); (C.M.); (O.O.)
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13
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Meewan I, Panmanee J, Petchyam N, Lertvilai P. HBCVTr: an end-to-end transformer with a deep neural network hybrid model for anti-HBV and HCV activity predictor from SMILES. Sci Rep 2024; 14:9262. [PMID: 38649402 PMCID: PMC11035669 DOI: 10.1038/s41598-024-59933-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024] Open
Abstract
Hepatitis B and C viruses (HBV and HCV) are significant causes of chronic liver diseases, with approximately 350 million infections globally. To accelerate the finding of effective treatment options, we introduce HBCVTr, a novel ligand-based drug design (LBDD) method for predicting the inhibitory activity of small molecules against HBV and HCV. HBCVTr employs a hybrid model consisting of double encoders of transformers and a deep neural network to learn the relationship between small molecules' simplified molecular-input line-entry system (SMILES) and their antiviral activity against HBV or HCV. The prediction accuracy of HBCVTr has surpassed baseline machine learning models and existing methods, with R-squared values of 0.641 and 0.721 for the HBV and HCV test sets, respectively. The trained models were successfully applied to virtual screening against 10 million compounds within 240 h, leading to the discovery of the top novel inhibitor candidates, including IJN04 for HBV and IJN12 and IJN19 for HCV. Molecular docking and dynamics simulations identified IJN04, IJN12, and IJN19 target proteins as the HBV core antigen, HCV NS5B RNA-dependent RNA polymerase, and HCV NS3/4A serine protease, respectively. Overall, HBCVTr offers a new and rapid drug discovery and development screening method targeting HBV and HCV.
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Affiliation(s)
- Ittipat Meewan
- Center for Advanced Therapeutics, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand.
| | - Jiraporn Panmanee
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Nopphon Petchyam
- Center for Advanced Therapeutics, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Pichaya Lertvilai
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
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14
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Al Khoury C, Tokajian S, Nemer N, Nemer G, Rahy K, Thoumi S, Al Samra L, Sinno A. Computational Applications: Beauvericin from a Mycotoxin into a Humanized Drug. Metabolites 2024; 14:232. [PMID: 38668360 PMCID: PMC11051850 DOI: 10.3390/metabo14040232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Drug discovery was initially attributed to coincidence or experimental research. Historically, the traditional approaches were complex, lengthy, and expensive, entailing costly random screening of synthesized compounds or natural products coupled with in vivo validation largely depending on the availability of appropriate animal models. Currently, in silico modeling has become a vital tool for drug discovery and repurposing. Molecular docking and dynamic simulations are being used to find the best match between a ligand and a molecule, an approach that could help predict the biomolecular interactions between the drug and the target host. Beauvericin (BEA) is an emerging mycotoxin produced by the entomopathogenic fungus Beauveria bassiana, being originally studied for its potential use as a pesticide. BEA is now considered a molecule of interest for its possible use in diverse biotechnological applications in the pharmaceutical industry and medicine. In this manuscript, we provide an overview of the repurposing of BEA as a potential therapeutic agent for multiple diseases. Furthermore, considerable emphasis is given to the fundamental role of in silico techniques to (i) further investigate the activity spectrum of BEA, a secondary metabolite, and (ii) elucidate its mode of action.
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Affiliation(s)
- Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos Campus, Byblos P.O. Box 36, Lebanon
| | - Nabil Nemer
- Department of Agriculture and Food Engineering, Holy Spirit University of Kaslik, Jounieh P.O. Box 446, Lebanon
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar
| | - Kelven Rahy
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos P.O. Box 36, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, Lebanese American University, Beirut P.O. Box 13-5053, Lebanon
| | - Lynn Al Samra
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Aia Sinno
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon
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15
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Fonseca-Benítez V, Acosta-Guzmán P, Sánchez JE, Alarcón Z, Jiménez RA, Guevara-Pulido J. Design and Evaluation of NSAID Derivatives as AKR1C3 Inhibitors for Breast Cancer Treatment through Computer-Aided Drug Design and In Vitro Analysis. Molecules 2024; 29:1802. [PMID: 38675620 PMCID: PMC11052204 DOI: 10.3390/molecules29081802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Breast cancer is a major global health issue, causing high incidence and mortality rates as well as psychological stress for patients. Chemotherapy resistance is a common challenge, and the Aldo-keto reductase family one-member C3 enzyme is associated with resistance to anthracyclines like doxorubicin. Recent studies have identified celecoxib as a potential treatment for breast cancer. Virtual screening was conducted using a quantitative structure-activity relationship model to develop similar drugs; this involved backpropagation of artificial neural networks and structure-based virtual screening. The screening revealed that the C-6 molecule had a higher affinity for the enzyme (-11.4 kcal/mol), a lower half-maximal inhibitory concentration value (1.7 µM), and a safer toxicological profile than celecoxib. The compound C-6 was synthesized with an 82% yield, and its biological activity was evaluated. The results showed that C-6 had a more substantial cytotoxic effect on MCF-7 cells (62%) compared to DOX (63%) and celecoxib (79.5%). Additionally, C-6 had a less harmful impact on healthy L929 cells than DOX and celecoxib. These findings suggest that C-6 has promising potential as a breast cancer treatment.
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Affiliation(s)
| | | | | | | | | | - James Guevara-Pulido
- Investigación en Química Aplicada INQA, Química Farmacéutica, Universidad El Bosque, Bogotá 11001, Colombia; (V.F.-B.); (Z.A.)
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16
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Ortega-Muñoz M, Alvarado S, Megia-Fernandez A, Hernandez-Mateo F, Lopez-Jaramillo FJ, Santoyo-Gonzalez F. Removal of Erythromycin from Water by Ibuprofen-Driven Pre-Organized Divinyl Sulfone Cross-Linked Dextrin. Polymers (Basel) 2024; 16:1090. [PMID: 38675010 PMCID: PMC11055069 DOI: 10.3390/polym16081090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Water recycling and reuse are cornerstones of water management, which can be compromised by the presence of pollutants. Among these, pharmaceuticals can overcome standard water treatments and require sophisticated approaches to remove them. Sorption is an economically viable alternative limited by the need for sorbents with a sorption coefficient (Kd) higher than 500 L/kg. The cross-linking of dextrin (Dx) with divinyl sulfone (DVS) in the presence of 1 mmol or 5 mmol of ibuprofen (IBU) yields the insoluble polymers pDx1 and pDx5 with improved affinity for IBU and high selectivity towards erythromycin (ERY) and ERY Kd higher than 4 × 103 L/kg, when tested against a cocktail of six drugs. Characterization of the polymers shows that both pDx1 and pDx5 have similar properties, fast sorption kinetics, and ERY Kd of 13.3 × 103 for pDx1 and 6.4 × 103 for pDx5, representing 26.6 and 12.0 times the 500 L/kg threshold. The fact that new affinities and improvements in Kd can be achieved by cross-linking Dx in the presence of other molecules that promote pre-organization expands the applications of DVS cross-linked polysaccharides as sustainable, scalable, and environmentally friendly sorbents with a potential application in wastewater treatment plants (WTPs).
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Affiliation(s)
- Mariano Ortega-Muñoz
- Department of Organic Chemistry, Faculty of Sciences, University of Granada, 18073 Granada, Spain
- Unit of Excellence in Chemistry Applied to Biomedicine and the Environment, University of Granada, 18073 Granada, Spain
- Biotechnology Institute, University of Granada, 18071 Granada, Spain
| | - Sarah Alvarado
- Department of Organic Chemistry, Faculty of Sciences, University of Granada, 18073 Granada, Spain
| | - Alicia Megia-Fernandez
- Department of Organic Chemistry, Faculty of Sciences, University of Granada, 18073 Granada, Spain
- Unit of Excellence in Chemistry Applied to Biomedicine and the Environment, University of Granada, 18073 Granada, Spain
- Biotechnology Institute, University of Granada, 18071 Granada, Spain
| | - Fernando Hernandez-Mateo
- Department of Organic Chemistry, Faculty of Sciences, University of Granada, 18073 Granada, Spain
- Unit of Excellence in Chemistry Applied to Biomedicine and the Environment, University of Granada, 18073 Granada, Spain
- Biotechnology Institute, University of Granada, 18071 Granada, Spain
| | - Francisco Javier Lopez-Jaramillo
- Department of Organic Chemistry, Faculty of Sciences, University of Granada, 18073 Granada, Spain
- Unit of Excellence in Chemistry Applied to Biomedicine and the Environment, University of Granada, 18073 Granada, Spain
- Biotechnology Institute, University of Granada, 18071 Granada, Spain
| | - Francisco Santoyo-Gonzalez
- Department of Organic Chemistry, Faculty of Sciences, University of Granada, 18073 Granada, Spain
- Unit of Excellence in Chemistry Applied to Biomedicine and the Environment, University of Granada, 18073 Granada, Spain
- Biotechnology Institute, University of Granada, 18071 Granada, Spain
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17
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Ahmad I, Huang PJ, Malak N, Khan A, Asad F, Chen CC. Antioxidant potential of alkaloids and polyphenols of Viola canescens wall using in vitro and in silico approaches. Front Chem 2024; 12:1379463. [PMID: 38680459 PMCID: PMC11045935 DOI: 10.3389/fchem.2024.1379463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/13/2024] [Indexed: 05/01/2024] Open
Abstract
Background: V. canescens Wall, a plant renowned for its ethno-medical properties, was investigated in this study for its antioxidant potential based on its wide therapeutic applications in traditional healthcare systems. The study aimed to assess the antioxidant potential of the plant extract/fractions and to predict the active phytochemicals using computational techniques. Methods: Five fractions were obtained from the crude methanolic extract of Viola canescens, and six concentrations (25, 50, 75, 100, 125, and 150 μg/mL) were prepared for each fraction. The antioxidant activity of these fractions was evaluated using the Tetraoxomolybdate (VI) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay. In-silico docking studies and molecular dynamic simulations were conducted to further elucidate the molecular interactions underlying the antioxidant activity. Results: The aqueous extract of V. canescens exhibited significant antioxidant and free radical scavenging activity against DPPH. Additionally, the crude flavonoid extract demonstrated moderate activity with IC50 value of 57.863 μg/mL, indicating potent inhibition of cell growth. In-silico docking studies revealed a strong interaction between emetine and the aromatase protein, suggesting its potential as an antioxidant. Conclusion: The study findings highlight the antioxidant potential of V. canescens extract, indicating its suitability as a source of natural antioxidants. These results suggest its potential application in pharmaceutical preparations aimed at harnessing antioxidant properties for therapeutic purposes.
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Affiliation(s)
- Imtiaz Ahmad
- Department of Botany, Bacha Khan University Charsadda, Charsadda, Pakistan
| | - Pin-Jui Huang
- Division of Surgical Intensive Care Unit, Department of Surgery, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Nosheen Malak
- Department of Zoology, Abdul Wali Khan University, Mardan, Pakistan
| | - Adil Khan
- Department of Botany, Bacha Khan University Charsadda, Charsadda, Pakistan
| | - Fayaz Asad
- Department of Botany, Bacha Khan University Charsadda, Charsadda, Pakistan
| | - Chien-Chin Chen
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
- Doctoral Program in Translational Medicine, Rong Hsing Translational Medicine Research Center, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
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18
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Drioiche A, Baammi S, Zibouh K, Al Kamaly O, Alnakhli AM, Remok F, Saidi S, Amaiach R, El Makhoukhi F, Elomri A, Zair T. A Study of the Synergistic Effects of Essential Oils from Origanum compactum and Origanum elongatum with Commercial Antibiotics against Highly Prioritized Multidrug-Resistant Bacteria for the World Health Organization. Metabolites 2024; 14:210. [PMID: 38668338 PMCID: PMC11051742 DOI: 10.3390/metabo14040210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
The irrational use of antibiotics has favored the emergence of resistant bacteria, posing a serious threat to global health. To counteract antibiotic resistance, this research seeks to identify novel antimicrobials derived from essential oils that operate through several mechanisms. It aims to evaluate the quality and composition of essential oils from Origanum compactum and Origanum elongatum; test their antimicrobial activity against various strains; explore their synergies with commercial antibiotics; predict the efficacy, toxicity, and stability of compounds; and understand their molecular interactions through docking and dynamic simulations. The essential oils were extracted via hydrodistillation from the flowering tops of oregano in the Middle Atlas Mountains in Morocco. Gas chromatography combined with mass spectrometry (GC-MS) was used to examine their composition. Nine common antibiotics were chosen and tested alone or in combination with essential oils to discover synergistic effects against clinically important and resistant bacterial strains. A comprehensive in silico study was conducted, involving molecular docking and molecular dynamics simulations (MD). O. elongatum oil includes borneol (8.58%), p-cymene (42.56%), thymol (28.43%), and carvacrol (30.89%), whereas O. compactum oil is mostly composed of γ-terpinene (22.89%), p-cymene (15.84%), thymol (10.21%), and (E)-caryophyllene (3.63%). With O. compactum proving to be the most potent, these essential oils showed antibacterial action against both Gram-positive and Gram-negative bacteria. Certain antibiotics, including ciprofloxacin, ceftriaxone, amoxicillin, and ampicillin, have been shown to elicit synergistic effects. To fight resistant bacteria, the essential oils of O. compactum and O. elongatum, particularly those high in thymol and (E)-caryophyllene, seem promising when combined with antibiotics. These synergistic effects could result from their ability to target the same bacterial proteins or facilitate access to target sites, as suggested by molecular docking simulations. Molecular dynamics simulations validated the stability of the examined protein-ligand complexes, emphasizing the propensity of substances like thymol and (E)-caryophyllene for particular target proteins, opening the door to potentially effective new therapeutic approaches against pathogens resistant to multiple drugs.
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Affiliation(s)
- Aziz Drioiche
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
- Medical Microbiology Laboratory, Mohamed V. Hospital, Meknes 50000, Morocco
| | - Soukayna Baammi
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco;
| | - Khalid Zibouh
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
| | - Omkulthom Al Kamaly
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; (O.A.K.); (A.M.A.)
| | - Anwar M. Alnakhli
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; (O.A.K.); (A.M.A.)
| | - Firdaous Remok
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
| | - Soukaina Saidi
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
| | - Rachid Amaiach
- Laboratory of Materials, Processes, Catalysis and Environment, School of Technology, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco;
| | - Fadoua El Makhoukhi
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
| | - Abdelhakim Elomri
- UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Normandie University, 76000 Rouen, France;
| | - Touriya Zair
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
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19
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Moin AT, Robin TB, Patil RB, Rani NA, Prome AA, Sakif TI, Hossain M, Chowdhury DUS, Rashid SS, Mollah AKMM, Islam S, Uddin MH, Khalequzzaman M, Islam T, Islam NN. Antifungal plant flavonoids identified in silico with potential to control rice blast disease caused by Magnaporthe oryzae. PLoS One 2024; 19:e0301519. [PMID: 38578751 PMCID: PMC10997076 DOI: 10.1371/journal.pone.0301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Rice blast disease, caused by the fungus Magnaporthe oryzae, poses a severe threat to rice production, particularly in Asia where rice is a staple food. Concerns over fungicide resistance and environmental impact have sparked interest in exploring natural fungicides as potential alternatives. This study aimed to identify highly potent natural fungicides against M. oryzae to combat rice blast disease, using advanced molecular dynamics techniques. Four key proteins (CATALASE PEROXIDASES 2, HYBRID PKS-NRPS SYNTHETASE TAS1, MANGANESE LIPOXYGENASE, and PRE-MRNA-SPLICING FACTOR CEF1) involved in M. oryzae's infection process were identified. A list of 30 plant metabolites with documented antifungal properties was compiled for evaluation as potential fungicides. Molecular docking studies revealed that 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin exhibited superior binding affinities compared to reference fungicides (Azoxystrobin and Tricyclazole). High throughput molecular dynamics simulations were performed, analyzing parameters like RMSD, RMSF, Rg, SASA, hydrogen bonds, contact analysis, Gibbs free energy, and cluster analysis. The results revealed stable interactions between the selected metabolites and the target proteins, involving important hydrogen bonds and contacts. The SwissADME server analysis indicated that the metabolites possess fungicide properties, making them effective and safe fungicides with low toxicity to the environment and living beings. Additionally, bioactivity assays confirmed their biological activity as nuclear receptor ligands and enzyme inhibitors. Overall, this study offers valuable insights into potential natural fungicides for combating rice blast disease, with 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin standing out as promising and environmentally friendly alternatives to conventional fungicides. These findings have significant implications for developing crop protection strategies and enhancing global food security, particularly in rice-dependent regions.
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Affiliation(s)
- Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Pune, Maharashtra, India
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Anindita Ash Prome
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Tahsin Islam Sakif
- Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, United States of America
| | - Mohabbat Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Dil Umme Salma Chowdhury
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Shah Samiur Rashid
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chattogram, Bangladesh
| | | | - Saiful Islam
- Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, Bangladesh
| | - Mohammad Helal Uddin
- Department of Applied Chemistry and Chemical Engineering, University of Chittagong, Chittagong, Bangladesh
| | | | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nazneen Naher Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
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20
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Mitchell SM, Heise RM, Murray ME, Lambo DJ, Daso RE, Banerjee IA. An investigation of binding interactions of tumor-targeted peptide conjugated polyphenols with the kinase domain of ephrin B4 and B2 receptors. Mol Divers 2024; 28:817-849. [PMID: 36847923 PMCID: PMC9969393 DOI: 10.1007/s11030-023-10621-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/02/2023] [Indexed: 03/01/2023]
Abstract
Recent studies have shown that Ephrin receptors may be upregulated in several types of cancers including breast, ovarian and endometrial cancers, making them a target for drug design. In this work, we have utilized a target-hopping approach to design new natural product-peptide conjugates and examined their interactions with the kinase-binding domain of EphB4 and EphB2 receptors. The peptide sequences were generated through point mutations of the known EphB4 antagonist peptide TNYLFSPNGPIA. Their anticancer properties and secondary structures were analyzed computationally. Conjugates of most optimum of peptides were then designed by binding the N-terminal of the peptides with the free carboxyl group of the polyphenols sinapate, gallate and coumarate, which are known for their inherent anticancer properties. To investigate if these conjugates have a potential to bind to the kinase domain, we carried out docking studies and MMGBSA free energy calculations of the trajectories based on the molecular dynamics simulations, with both the apo and the ATP bound kinase domains of both receptors. In most cases binding interactions occurred within the catalytic loop region, while in some cases the conjugates were found to spread out across the N-lobe and the DFG motif region. The conjugates were further tested for prediction of pharmacokinetic properties using ADME studies. Our results indicated that the conjugates were lipophilic and MDCK permeable with no CYP interactions. These findings provide an insight into the molecular interactions of these peptides and conjugates with the kinase domain of the EphB4 and EphB2 receptor. As a proof of concept, we synthesized and carried out SPR analysis with two of the conjugates (gallate-TNYLFSPNGPIA and sinapate-TNYLFSPNGPIA). Results indicated that the conjugates showed higher binding with the EphB4 receptor and minimal binding to EphB2 receptor. Sinapate-TNYLFSPNGPIA showed inhibitory activity against EphB4. These studies reveal that some of the conjugates may be developed for further investigation into in vitro and in vivo studies and potential development as therapeutics.
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Affiliation(s)
- Saige M Mitchell
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Ryan M Heise
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Molly E Murray
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Dominic J Lambo
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Rachel E Daso
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Ipsita A Banerjee
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA.
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21
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Ashok AK, Gnanasekaran TS, Santosh Kumar HS, Srikanth K, Prakash N, Gollapalli P. High-throughput screening and molecular dynamics simulations of natural products targeting LuxS/AI-2 system as a novel antibacterial strategy for antibiotic resistance in Helicobacter pylori. J Biomol Struct Dyn 2024; 42:2913-2928. [PMID: 37160706 DOI: 10.1080/07391102.2023.2210674] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/25/2023] [Indexed: 05/11/2023]
Abstract
The main goal of treating any Helicobacter pylori (H. pylori)-related gastrointestinal disease is completely eradicating infection. Falling eradication efficiency, off-target effects, and patient noncompliance with prolonged and broad spectrums have sparked clinical interest in exploring other effective, safer therapeutic choices. As natural substances are risk-free and privileged with high levels of antibacterial activity, most of these natural chemical's specific modes of action are unknown. With the aid of in silico molecular docking-based virtual screening studies and molecular dynamic simulations, the current study is intended to gather data on numerous such natural chemicals and assess their affinity for the S-ribosyl homocysteine lyase (LuxS) protein of H. pylori. The ligand with the highest binding energy with LuxS, glucoraphanin, catechin gallate and epigallocatechin gallate were rationally selected for further computational analysis. The solution stability of the three compounds' optimal docking postures with LuxS was initially assessed using long-run molecular dynamics simulations. Using molecular dynamics simulation, the epigallocatechin gallate was found to be the most stable molecule with the highest binding free energy, indicating that it might compete with the natural ligand of the inhibitors. According to ADMET analysis, his phytochemical was a promising therapeutic candidate for an antibacterial action since it had a range of physicochemical, pharmacokinetic, and drug-like qualities and had no discernible adverse effects. Additional in vitro, in vivo, and clinical trials are needed to confirm the drug's precise efficacy during H. pylori infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Avinash Karkada Ashok
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, India
| | - Tamizh Selvan Gnanasekaran
- Central Research Laboratory, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore, Karnataka, India
| | | | - Koigoora Srikanth
- Department of Biotechnology, Vignans Foundation for Science, Research and Technology (Deemed to be University), Guntur, Andhra Pradesh, India
| | - Nayana Prakash
- Department of Biotechnology and Bioinformatics, Jnana Sahyadri campus, Kuvempu University, Shankaraghatta, Karnataka, India
| | - Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangalore, Karnataka, India
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22
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Debnath S, Nath M, Sarkar A, Roy G, Chakraborty SK, Debnath B. Phytochemical characterization of Styrax benzoin resin extract, molecular docking, ADME, and antibacterial activity study. Nat Prod Res 2024; 38:1263-1268. [PMID: 36214683 DOI: 10.1080/14786419.2022.2132244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/17/2022] [Accepted: 09/27/2022] [Indexed: 10/17/2022]
Abstract
Styrax benzoin fumes have a spiritual aspect from ancient times, magical essence like a pleasant perfume, and are employed in religious ceremonies in India. This study aims to identify the volatile compounds in S. benzoin extract, their binding affinity to the bacterial target proteins, and study the antibacterial activity of the potential extract. The compounds obtained from GC-MS analysis of S. benzoin extract were subjected to molecular docking studies against DHFR of Staphylococcus aureus, tRNA synthetase of Escherichia coli, DHPS of Mycobacterium tuberculosis. Molecular docking studies revealed that seventeen compounds out of 20 compounds exhibited higher binding affinity than co-ligand (-7.00 kcal/mol) against the Staphylococcus aureus enzyme DHFR. Consequently, the crude extracts were evaluated for antibacterial activity against S. aureus, and the acetone extract showed promising findings. S. benzoin fumes might replace synthetic room fresheners, and promising compounds could be exploited in the cosmetics industry.
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Affiliation(s)
- Sudhan Debnath
- Department of Chemistry, Netaji Subhash Mahavidyalaya, Udaipur, India
| | - Moumita Nath
- Department of Forestry and Biodiversity, Tripura University, Agartala, India
| | - Alekhya Sarkar
- Department of Forestry and Biodiversity, Tripura University, Agartala, India
| | - Gourab Roy
- Department of Zoology, MBB College, Agartala, India
| | | | - Bimal Debnath
- Department of Forestry and Biodiversity, Tripura University, Agartala, India
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23
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Utami PD, Setianingsih H, Sari DRT. In Silico Approach Triterpene Glycoside of H. atra Targeting Orotidine 5-Monophosphate Decarboxylase Protein (PfOMPDC) in P. falciparum Infection Mechanism. BIOMED RESEARCH INTERNATIONAL 2024; 2024:5924799. [PMID: 38590385 PMCID: PMC11001475 DOI: 10.1155/2024/5924799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/31/2023] [Accepted: 02/12/2024] [Indexed: 04/10/2024]
Abstract
This study accessed the potential antimalarial activity of triterpene glycoside of H. atra through targeting orotidine 5-monophosphate decarboxylase protein (PfOMPDC) in P. falciparum by molecular docking. Nine triterpene glycosides from H. atra extract modeled the structure by the Corina web server and interacted with PfOMPDC protein by using Hex 8.0.0. The docking results were visualized and analyzed by Discovery Studio version 21.1.1. 17-Hydroxyfuscocineroside B showed the lowest binding energy in PfOMPDC interaction, which was -1,098.13 kJ/mol. Holothurin A3, echinoside A, and fuscocineroside C showed low binding energy. Nine triterpene glycosides of H. atra performed interaction with PfOMPDC protein at the same region. Holothurin A1 posed interaction with PfOMPDC protein by 8 hydrogen bonds, 3 hydrophobic interactions, and 8 unfavorable bonds. Several residues were detected in the same active sites of other triterpene glycosides. Residue TYR111 was identified in all triterpene glycoside complexes, except holothurin A3 and calcigeroside B. In summary, the triterpene glycoside of H. atra is potentially a drug candidate for malaria therapeutic agents. In vitro and in vivo studies were required for further investigation.
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Affiliation(s)
- Prawesty Diah Utami
- Parasitology Departement, Faculty of Medicine, Hang Tuah University, Surabaya, Indonesia
| | - Herin Setianingsih
- Anatomy and Histology Departement, Faculty of Medicine, Hang Tuah University, Surabaya, Indonesia
| | - Dewi Ratih Tirto Sari
- Pharmacy Department, Faculty of Medical Science, Ibrahimy University, Situbondo, Indonesia
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24
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Ibrahim BT, Allam HA, El-Dydamony NM, Fouad MA, Mohammed ER. Exploring new quinazolin-4(3H)-one derivatives as CDK2 inhibitors: Design, synthesis, and anticancer evaluation. Drug Dev Res 2024; 85:e22163. [PMID: 38419305 DOI: 10.1002/ddr.22163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/13/2024] [Accepted: 02/10/2024] [Indexed: 03/02/2024]
Abstract
In the present work, five series of new 2,3-disubstituted quinazolin-4(3H)-ones 4a-c, 5a-d, 6a-g, 7a,b, and 9a-c were designed, synthesized, and screened in vitro for their cytotoxic activity against 60 cancer cell lines by the National Cancer Institute, USA. Five candidates 4c, 6a, 6b, 6d, and 6g revealed promising cytotoxicity with significant percentage growth inhibition in the range of 81.98%-96.45% against the central nervous system (CNS) (SNB-19), melanoma (MDA-MB-435), and non-small cell lung cancer (HOP-62) cell lines. The in vitro cytotoxic half maximal inhibitory concentration (IC50 ) values for the most active compounds 4c, 6a, 6b, 6d, and 6g against the most sensitive cell lines were evaluated. Additionally, screening their cyclin-dependent kinase 2 (CDK2) inhibitory activity was performed. Ortho-chloro-benzylideneamino derivative 6b emerged as the most potent compound with IC50 = 0.67 µM compared to Roscovitine (IC50 = 0.64 µM). The most active candidates arrested the cell cycle at G1, S phases, or both, leading to cell death and inducing apoptosis against CNS (SNB-19), melanoma (MDA-MB-435), and non-small cell lung cancer (HOP-62) cell lines. The molecular docking study verified the resulting outcomes for the most active candidates in the CDK2-binding pocket. Finally, physicochemical, and pharmacokinetic properties deduced that compounds 4c, 6a, 6b, 6d, and 6g displayed significant drug-likeness properties. According to the obtained results, the newly targeted compounds are regarded as promising scaffolds for the continued development of novel CDK2 inhibitors.
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Affiliation(s)
- Basant T Ibrahim
- Pharmaceutical Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6th of October City, Egypt
| | | | - Nehad M El-Dydamony
- Pharmaceutical Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6th of October City, Egypt
| | - Marwa A Fouad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Pharmaceutical Chemistry Department, New Giza University, Cairo, Egypt
| | - Eman R Mohammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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25
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Alghamdi SS, Alghashem SA, Ali R, Alsubait A, Suliman RS, Mohammed AE, Alehaideb Z, Alshafi RA, Alturki AY, Rahman I. Exploring the potential of Ziziphus nummularia and luteolin-7-O-glucoside as tubulin inhibitors in cancer therapy and survival. Sci Rep 2024; 14:7202. [PMID: 38531974 DOI: 10.1038/s41598-024-57680-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
Cancer is responsible for approximately 10 million deaths worldwide, with 70% of the deaths occurring in low- and middle-income countries; as such safer and more effective anti-cancer drugs are required. Therefore, the potential benefits of Ziziphus nummularia and Ziziphus spina-christi as sources of anti-cancer agents were investigated. Z. nummularia and Z. spina-christi extracts were prepared using chloroform, ethanol, ethyl acetate, and water. The extracts' anti-cancer properties were determined using the MTT Cell Viability Assay in four cancer cell lines: breast (KAIMRC2 and MDA-MB-231), colorectal (HCT8), and liver (HepG2). The ApoTox-Glo Triplex Assay and high-content imaging (HCI)-Apoptosis Assay were used to assess KAIMRC2 and HCT8 cells further. In addition, KAIMRC2 cells were tested for microtubule staining, and AKT/mTOR protein expression was determined by western blot analysis. Liquid chromatography-mass spectrometry (LC-MS) was performed to identify the secondary metabolites in the ethanol and ethyl acetate extracts, followed by in silico techniques to predict molecular targets and interactions, safety, and pharmacokinetic profile for identified metabolites. Out of the eight extracts, the ethanolic extract of Z. nummularia, exhibited the most potent activity against KAIMRC2 cells with an IC50 value of 29.2 μg/ml. Cancer cell treatment with the ethanolic extract of Z. nummularia resulted in a dose-dependent decrease in cell viability with increased apoptosis and cytotoxic effects. Microtubule staining showed a disrupted microtubular network. The ethanolic extract treatment of KAIMRC2 cells led to upregulated expression of pAKT and pmTOR. In silico studies predicted luteolin-7-O-glucoside to be a ligand for tubulin with the highest docking score (- 7.686) and similar binding interactions relative to the native ligand. Further computational analysis of the metabolites showed acceptable pharmacokinetic and safety profiles, although ethanolic extract metabolites were predicted to have cardiotoxic effects. Ethanolic extraction is optimal for solubilizing active anticancer metabolites from Z. nummularia, which may act by causing M-phase arrest via inhibition of tubulin polymerization. Luteolin-7-O-glucoside is the lead candidate for further research and development as an anti-cancer agent. In addition, this study suggests that herbal treatment could switch on mechanisms of adaptation and survival in cancer cells.
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Affiliation(s)
- Sahar Saleh Alghamdi
- Pharmaceutical Sciences Department, College of Pharmacy, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Kingdom of Saudi Arabia
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs, Riyadh, Kingdom of Saudi Arabia
- King Abdulaziz Medical City, Ministry of the National Guard-Health Affairs, 11426, Riyadh, Kingdom of Saudi Arabia
| | - Sara Abdulaziz Alghashem
- Pharmaceutical Sciences Department, College of Pharmacy, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Rizwan Ali
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs, Riyadh, Kingdom of Saudi Arabia
| | - Arwa Alsubait
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs, Riyadh, Kingdom of Saudi Arabia
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Rasha Saad Suliman
- Pharmacy Department, Fatima College of Health Sciences (FCHS), Abu Dhabi, United Arab Emirates
| | - Afrah E Mohammed
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University (PNU), P.O. Box 84428, 11671, Riyadh, Kingdom of Saudi Arabia
| | - Zeyad Alehaideb
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs, Riyadh, Kingdom of Saudi Arabia
- King Abdulaziz Medical City, Ministry of the National Guard-Health Affairs, 11426, Riyadh, Kingdom of Saudi Arabia
| | - Raghad Abdullah Alshafi
- Pharmaceutical Sciences Department, College of Pharmacy, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Allulu Yousef Alturki
- Pharmaceutical Sciences Department, College of Pharmacy, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Ishrat Rahman
- Department of Basic Dental Sciences, College of Dentistry, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, 11671, Riyadh, Kingdom of Saudi Arabia.
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26
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Metwally HM, Younis NM, Abdel-Latif E, El-Rayyes A. New thiazole, thiophene and 2-pyridone compounds incorporating dimethylaniline moiety: synthesis, cytotoxicity, ADME and molecular docking studies. BMC Chem 2024; 18:52. [PMID: 38486282 PMCID: PMC10941513 DOI: 10.1186/s13065-024-01136-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 02/05/2024] [Indexed: 03/17/2024] Open
Abstract
Various sets of thiazole, thiophene, and 2-pyridone ring structures containing a dimethylaniline component were synthesized. Substituted thiazoles 2-3 and thiophenes 5-7 were produced by reacting thiocarbamoyl compound 4 with α-halogenated reagents in different basic conditions. Also, a series of 2-pyridone derivatives 9a-f substituted with dimethylaniline was synthesized through Michael addition of malononitrile to α,β-unsaturated nitrile derivatives 8a-f. The synthesized products were structurally proven by spectroscopic methods such as IR, 1H NMR, 13C NMR, and MS data. Furthermore, the anti-cancer efficacy of the compounds was assessed using the MTT assay on two cell lines: hepatocellular carcinoma (HepG-2) and breast cancer (MDA-MB-231). The results showed the highest growth inhibition for derivatives 2, 6, 7, and 9c, which were further examined for their IC50 values. The IC50 for compound 2 showed equipotent activity (IC50 = 1.2 µM) against the HepG-2 cell line compared to Doxorubicin (IC50 = 1.1 µM). Compounds 2, 6, 7 and 9c showed very good ADME assessments for further drug administration. Moreover, the PASS theoretical prediction for the compounds showed high antimitotic and antineoplastic activities for compounds 2, 6, 7, and 9c, as well as potent inhibition activity for the insulysin enzyme (IDE). Molecular docking stimulations were performed on CDK1/CyclinB1/CKS2 (PDB ID: 4y72) and BPTI (PDB ID: 2ra3). When docked into (PDB ID: 4y72), all of the tested compounds showed considerable inhibition, and the 2-pyridone derivative 9d had the maximum binding affinity (- 8.1223 kcal/mol). While thiophene derivative 6 offered the maximum binding affinity (- 7.5094 kcal/mol) when docked into (PDB ID: 2ra3).
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Affiliation(s)
- Heba M Metwally
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
| | - Norhan M Younis
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Ehab Abdel-Latif
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Ali El-Rayyes
- Department of Chemistry, Faculty of Science, Northern Border University, 1321, Arar, Saudi Arabia.
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27
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Montejo-López W, Sampieri-Cabrera R, Nicolás-Vázquez MI, Aceves-Hernández JM, Razo-Hernández RS. Analysing the effect caused by increasing the molecular volume in M1-AChR receptor agonists and antagonists: a structural and computational study. RSC Adv 2024; 14:8615-8640. [PMID: 38495977 PMCID: PMC10938299 DOI: 10.1039/d3ra07380g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
M1 muscarinic acetylcholine receptor (M1-AChR), a member of the G protein-coupled receptors (GPCR) family, plays a crucial role in learning and memory, making it an important drug target for Alzheimer's disease (AD) and schizophrenia. M1-AChR activation and deactivation have shown modifying effects in AD and PD preclinical models, respectively. However, understanding the pharmacology associated with M1-AChR activation or deactivation is complex, because of the low selectivity among muscarinic subtypes, hampering their therapeutic applications. In this regard, we constructed two quantitative structure-activity relationship (QSAR) models, one for M1-AChR agonists (total and partial), and the other for the antagonists. The binding mode of 59 structurally different compounds, including agonists and antagonists with experimental binding affinity values (pKi), were analyzed employing computational molecular docking over different structures of M1-AChR. Furthermore, we considered the interaction energy (Einter), the number of rotatable bonds (NRB), and lipophilicity (ilogP) for the construction of the QSAR model for agonists (R2 = 89.64, QLMO2 = 78, and Qext2 = 79.1). For the QSAR model of antagonists (R2 = 88.44, QLMO2 = 82, and Qext2 = 78.1) we considered the Einter, the fraction of sp3 carbons fCsp3, and lipophilicity (MlogP). Our results suggest that the ligand volume is a determinant to establish its biological activity (agonist or antagonist), causing changes in binding energy, and determining the affinity for M1-AChR.
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Affiliation(s)
- Wilber Montejo-López
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México Avenida 1o de Mayo s/n, Colonia Santa María las Torres Cuautitlán Izcalli Estado de Mexico 54740 Mexico
| | - Raúl Sampieri-Cabrera
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Centro de Ciencias de Complejidad, Universidad Nacional Autónoma de México Mexico
| | - María Inés Nicolás-Vázquez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México Avenida 1o de Mayo s/n, Colonia Santa María las Torres Cuautitlán Izcalli Estado de Mexico 54740 Mexico
| | - Juan Manuel Aceves-Hernández
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México Cuautitlán Izcalli Estado de Mexico 54714 Mexico
| | - Rodrigo Said Razo-Hernández
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos Av. Universidad 1001 Cuernavaca 62209 Mexico
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28
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Ahmad Ansari I, Debnath B, Kar S, Patel HM, Debnath S, Zaki MEA, Pal P. Identification of potential edible spices as EGFR and EGFR mutant T790M/L858R inhibitors by structure-based virtual screening and molecular dynamics. J Biomol Struct Dyn 2024; 42:2464-2481. [PMID: 37349948 DOI: 10.1080/07391102.2023.2223661] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/14/2023] [Indexed: 06/24/2023]
Abstract
Epidermal growth factor receptor (EGFR) tyrosine kinases are overexpressed in several human cancers and could serve as a promising anti-cancer drug target. With this in view, the main aim of the present study was to identify spices having the potential to inhibit EGFR tyrosine kinase. The structure-based virtual screening of spice database consisting of 1439 compounds with EGFR tyrosine kinase (PDB ID: 3W32) was carried out using Glide. Top scored 18 hits (XP Glide Score ≥ -10.0 kcal/mol) was further docked with three EGFR tyrosine kinases and three EGFR T790M/L858R mutants using AutodockVina, followed by ADME filtration. The best three hits were further refined by Molecular Dynamics (MD) simulation and MM-GBSA-based binding energy calculation. The overall docking results of the selected hits with both EGFR and EGFR T790M/L858R were quite satisfactory and showed strong binding compared to the three coligands. Detailed MD analysis of CL_07, AC_11 and AS_49 also showed the stability of the protein-ligand complexes. Moreover, the hits were drug-like, and MM-GBSA binding free energy of CL_07 and AS_49 was established to be far better. AC_11 was found to be similar to the known inhibitor Gefitinib. Most of the potential hits are available in Allium cepa, CL_07 and AS_49 available in Curcuma longa and Allium sativum, respectively. Therefore, these three spices could be used as a potential therapeutic candidate against cancer caused by overexpression of EGFR after validation of the observations of this study in in-vitro experiments. Further extensive work is needed to improve the scaffolds CL_07, AC_11, AC_17, and AS_49 as potential anti-cancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Iqrar Ahmad Ansari
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, India
- Division of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, India
| | - Bimal Debnath
- Department of Forestry and Biodiversity, Tripura University, Suryamaninagar, Tripura, India
| | - Saikat Kar
- Department of Obstetrics and Gynecology, Agartala Govt. Medical College, Tripura, India
| | - Harun M Patel
- Division of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur (Dhule), Maharashtra, India
| | - Sudhan Debnath
- Department of Chemistry, Netaji Subhas Mahavidyalaya, Udaipur, Tripura, India
| | - Magdi E A Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University, Faculty of Science, Riyadh, Saudi Arabia
| | - Pinaki Pal
- Department of Physics, RamkrishnaMahavidyalay, Unokoti, Tripura, India
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29
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Awuni E, Abdallah Musah R. Proposing lead compounds for the development of SARS-CoV-2 receptor-binding inhibitors. J Biomol Struct Dyn 2024; 42:2282-2297. [PMID: 37116068 DOI: 10.1080/07391102.2023.2204505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 04/11/2023] [Indexed: 04/30/2023]
Abstract
The COVID-19 pandemic has had deleterious effects on the world and demands urgent measures to find therapeutic agents to combat the current and related future outbreaks. The entry of SARS-CoV-2 into the host's cell is facilitated by the interaction between the viral spike receptor-binding domain (sRBD) and the human angiotensin-converting enzyme 2 (hACE2). Although the interface of sRBD involved in the sRBD-hACE2 interaction has been projected as a primary vaccine and drug target, currently no small-molecule drugs have been approved for covid-19 treatment targeting sRBD. Herein structure-based virtual screening and molecular dynamics (MD) simulation strategies were applied to identify novel potential small-molecule binders of the SARS-CoV-2 sRBD from an sRBD-targeted compound library as leads for the development of anti-COVID-19 drugs. The library was initially screened against sRBD by using the GOLD docking program whereby 19 compounds were shortlisted based on docking scores after using a control compound to set the selection cutoff. The stability of each compound in MD simulations was used as a further standard to select four hits namely T4S1820, T4589, E634-1449, and K784-7078. Analyses of simulations data showed that the four compounds remained stably bound to sRBD for ≥ 80 ns with reasonable affinities and interacted with pharmacologically important amino acid residues. The compounds exhibited fair solubility, lipophilicity, and toxicity-propensity characteristics that could be improved through lead optimization regimes. The overall results suggest that the scaffolds of T4S1820, E634-1449, and K784-7078 could serve as seeds for developing potent small-molecule inhibitors of SARS-CoV-2 receptor binding and cell entry.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elvis Awuni
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
| | - Radiatu Abdallah Musah
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
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30
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Liu R, Chen X, Li J, Liu X, Shu M. Discovery of novel bromodomain-containing protein 4 (BRD4-BD1) inhibitors combined with 3d-QSAR, molecular docking and molecular dynamics in silico. J Biomol Struct Dyn 2024:1-18. [PMID: 38425011 DOI: 10.1080/07391102.2024.2321249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Bromine-containing domain protein 4 (BRD4) plays a crucial role in regulating transcription and genome stability. Selective inhibitors of BRD4-BD1 can specifically target specific bromine domains to affect cell proliferation, apoptosis, and differentiation. In this work, 43 selective benzoazepinone BRD4-BD1 inhibitors were studied using molecular simulations and three-dimensional quantitative conformation relationships (3D-QSAR). A reliable 3D-QSAR model was established based on COMFA (Q2 = 0.532, R2 = 0.981) and COMSIA (S + E + H (Q2 = 0.536, R2 = 0.979) two different analysis methods. Through 3D-QSAR model prediction and quantum chemical analysis, 15 small molecules with stronger inhibitory activity than the template compounds were constructed, and 5 new compounds with higher predictive activity and binding affinity were screened by molecular docking and ADMET methods. According to the molecular dynamics simulation, the key residues that can interact with BRD4-BD1 protein and molecular docking results are consistent, including ASN140, MET132, GLN85, MET105, ASN135 and TYR97. From the MD trajectory, we calculated and analyzed RMSD, RMSF, free binding energy, FECM, DCCM and PCA, the loop region formed by amino acids VAL45∼PRO62 showed α-helix, β-folding and clustering towards the active center with the extension of simulation time. Further optimization of the structure of active candidate compounds A6, A11, A14, and A15 will provide the necessary theoretical basis for the synthesis and activity evaluation of novel BRD4-BD1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rong Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Xiaodie Chen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Jiali Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Xingyun Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
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31
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Abbade Y, Kisla MM, Hassan MAK, Celik I, Dogan TS, Mutlu P, Ates-Alagoz Z. Synthesis, Anticancer Activity, and In Silico Modeling of Alkylsulfonyl Benzimidazole Derivatives: Unveiling Potent Bcl-2 Inhibitors for Breast Cancer. ACS OMEGA 2024; 9:9547-9563. [PMID: 38434899 PMCID: PMC10905736 DOI: 10.1021/acsomega.3c09411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/26/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
A series of alkylsulfonyl 1H-benzo[d]imidazole derivatives were synthesized and evaluated for anticancer activity against human breast cancer cells, MCF-7 in vitro. The cytotoxic potential was determined using the xCELLigence real-time cell analysis, and expression levels of genes related to microtubule organization, tumor suppression, apoptosis, cell cycle, and proliferation were examined by quantitative real-time polymerase chain reaction. Molecular docking against Bcl-2 was carried out using AutoDock Vina, while ADME studies were performed to predict the physicochemical and drug-likeness properties of the synthesized compounds. The results revealed that compounds 23 and 27 were the most potent cytotoxic derivatives against MCF-7 cells. Gene expression analysis showed that BCL-2 was the most prominent gene studied. Treatment of MCF-7 cells with compounds 23 and 27 resulted in significant downregulation of the BCL-2 gene, with fold changes of 128 and 256, respectively. Docking analysis predicted a strong interaction between the compounds and the target protein. Interestingly, all of the compounds exhibit a higher binding affinity toward Bcl-2 than the standard drug (compound 27 vina score = -9.6 kcal/mol, vincristine = -6.7 kcal/mol). Molecular dynamics simulations of compounds 23 and 27 showed a permanent stabilization in the binding site of Bcl-2 for 200 ns. Based on Lipinski and Veber's filters, all synthesized compounds displayed drug-like characteristics. These findings suggest that compounds 23 and 27 were the most promising cytotoxic compounds and downregulated the expression of the BCL-2 gene. These derivatives could be further explored as potential candidates for the treatment of breast cancer.
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Affiliation(s)
- Yemna Abbade
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100 Ankara, Turkey
- Graduate
School of Health Sciences, Ankara University, 06110 Ankara, Turkey
| | - Mehmet Murat Kisla
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100 Ankara, Turkey
- Graduate
School of Health Sciences, Ankara University, 06110 Ankara, Turkey
| | - Mohammed Al-Kassim Hassan
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100 Ankara, Turkey
- Graduate
School of Health Sciences, Ankara University, 06110 Ankara, Turkey
- Department
of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical
Sciences, Bayero University, P.M.B 3011 Kano, Nigeria
| | - Ismail Celik
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
| | - Tugba Somay Dogan
- Central
Laboratory, Molecular Biology and Biotechnology R&D Center, Middle East Technical University, 06800 Ankara, Turkey
| | - Pelin Mutlu
- Department
of Biotechnology, Biotechnology Institute, Ankara University, 06135 Ankara, Turkey
| | - Zeynep Ates-Alagoz
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100 Ankara, Turkey
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32
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Mohamed SK, Siddique SA, Karthikeyan S, Ahmed EA, Omran OA, Mague JT, Al-Salahi R, El Bakri Y. Synthesis, X-ray crystallography, computational investigation on quinoxaline derivatives as potent against adenosine receptor A2AAR. J Biomol Struct Dyn 2024:1-19. [PMID: 38385483 DOI: 10.1080/07391102.2024.2314268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/28/2024] [Indexed: 02/23/2024]
Abstract
Quinoxaline represents one of the most important classes of heterocyclic compounds, which have exhibited a wide range of biological activities and industrial importance in many different fields. In this regard, we have synthetized two new quinoxaline derivatives. Their structures were confirmed by single-crystal X-ray analysis. The compounds show potent activity against adenosine receptors A2AAR based on structural activity relationship studies. Further molecular docking, molecular dynamics, ADMET analysis, and DFT (density functional theory) calculations were performed to understand the titled compound's future drug candidacy. DFT computations confirmed the good stability of the synthesized compounds, as evidenced by the optimized molecular geometry, HOMO-LUMO energy gap, and intermolecular interactions. NBO analysis confirmed intermolecular interactions mediated by lone pair, bonding, and anti-bonding orbitals. All DFT findings were consistent with experimental results, indicating that the synthesized molecules are highly stable. These findings suggest that the synthesized compounds are promising candidates for further development as drugs for the treatment of A2AAR-related diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, England
| | - Sabir Ali Siddique
- Institute of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, Bahawalpur, Pakistan
| | - Subramani Karthikeyan
- Centre for Healthcare Advancement, Innovation and Research, Vellore Institute of Technology University, Chennai Campus, Chennai, Tamil Nadu, India
| | - Eman A Ahmed
- Department of Chemistry, Faculty of Science, Sohag University, Sohag, Egypt
| | - Omran A Omran
- Department of Chemistry, Faculty of Science, Sohag University, Sohag, Egypt
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
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Bryndal I, Stolarczyk M, Mikołajczyk A, Krupińska M, Pyra A, Mączyński M, Matera-Witkiewicz A. Pyrimidine Schiff Bases: Synthesis, Structural Characterization and Recent Studies on Biological Activities. Int J Mol Sci 2024; 25:2076. [PMID: 38396753 PMCID: PMC10889512 DOI: 10.3390/ijms25042076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Recently, 5-[(4-ethoxyphenyl)imino]methyl-N-(4-fluorophenyl)-6-methyl-2-phenylpyrimidin-4-amine has been synthesized, characterized, and evaluated for its antibacterial activity against Enterococcus faecalis in combination with antineoplastic activity against gastric adenocarcinoma. In this study, new 5-iminomethylpyrimidine compounds were synthesized which differ in the substituent(s) of the aromatic ring attached to the imine group. The structures of newly obtained pyrimidine Schiff bases were established by spectroscopy techniques (ESI-MS, FTIR and 1H NMR). To extend the current knowledge about the features responsible for the biological activity of the new 5-iminomethylpyrimidine derivatives, low-temperature single-crystal X-ray analyses were carried out. For all studied crystals, intramolecular N-H∙∙∙N hydrogen bonds and intermolecular C-H∙∙∙F interactions were observed and seemed to play an essential role in the formation of the structures. Simultaneously, their biological properties based on their cytotoxic features were compared with the activities of the Schiff base (III) published previously. Moreover, computational investigations, such as ADME prediction analysis and molecular docking, were also performed on the most active new Schiff base (compound 4b). These results were compared with the highest active compound III.
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Affiliation(s)
- Iwona Bryndal
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (M.S.); (M.M.)
| | - Marcin Stolarczyk
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (M.S.); (M.M.)
| | - Aleksandra Mikołajczyk
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (A.M.); (M.K.); (A.M.-W.)
| | - Magdalena Krupińska
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (A.M.); (M.K.); (A.M.-W.)
| | - Anna Pyra
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie, 50-383 Wrocław, Poland;
| | - Marcin Mączyński
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (M.S.); (M.M.)
| | - Agnieszka Matera-Witkiewicz
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (A.M.); (M.K.); (A.M.-W.)
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Hanifa B, Bibi N, Sirajuddin M, Tiekink ERT, Kubicki M, Khan I, Bari A, Wadood A, Shams S. Synthesis, spectral characterisation, biocidal investigation, in-silico and molecular docking studies of 4-[(2-chloro-4-methylphenyl)carbamoyl]butanoic acid derived triorganotin(IV) compounds. J Biomol Struct Dyn 2024; 42:1826-1845. [PMID: 37114651 DOI: 10.1080/07391102.2023.2204160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/08/2023] [Indexed: 04/29/2023]
Abstract
Three triorganotin(IV) compounds, R3Sn(L), with R = CH3 (1), n-C4H9 (2) and C6H5 (3), and LH = 4-[(2-chloro-4-methylphenyl)carbamoyl]butanoic acid, were prepared and confirmed by various techniques. A five-coordinate, distorted trigonal-bipyramidal geometry was elucidated for tin(IV) centres both in solution and solid states. An intercalation mode was confirmed for the compound SS-DNA interaction by UV-visible, viscometric techniques and molecular docking. MD simulation revealed stable binding of LH with SS-DNA. Anti-bacterial investigation revealed 2 to be generally the most potent, especially against Sa and Ab, i.e. having the lowest MIC values (≤0.25 μg/mL) compared to the standard anti-biotics vancomycin-HCl (MIC = 1 μg/mL) and colistin-sulphate (MIC = 0.25 μg/mL). Similarly, the anti-fungal profile shows 2 exhibits 100% inhibition against Ca and Cn fungal strains and has MIC values (≤0.25 μg/mL) comparatively lower than standard drug fluconazole (0.125 and 8 μg/mL for Ca and Cn, respectively). Compound 2 has the greatest activity with CC50 ≤ 25 μg/mL and HC50 > 32 μg/mL performed against HEC239 and RBC cell lines. The anti-cancer potential was assessed against the MG-U87 cell line, using cisplatin as the standard (133 µM), indicates 2 displays the greatest activity (IC50: 5.521 µM) at a 5 µM dose. The greatest anti-leishmanial potential was observed for 2 (87.75 at 1000 μg/mL) in comparison to amphotericin B (90.67). The biological assay correlates with the observed maximum of 89% scavenging activity exhibited by 2. The Swiss-ADME data publicised the screened compounds generally follow the rule of 5 of drug-likeness and have good bioavailability potential.
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Affiliation(s)
- Bibi Hanifa
- Department of Chemistry, University of Science & Technology, Bannu, Pakistan
| | - Naila Bibi
- Department of Chemistry, University of Science & Technology, Bannu, Pakistan
| | - Muhammad Sirajuddin
- Department of Chemistry, University of Science & Technology, Bannu, Pakistan
| | - Edward R T Tiekink
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Maciej Kubicki
- Department of Chemistry, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Ishaq Khan
- Cancer Cell Culture & Precision Oncomedicine Lab, Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
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35
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Beg MZ, Singh PK, Singh PP, Srivastava M, Srivastava V. Metal-free visible light mediated direct C-H amination of benzoxazole with secondary amines. Mol Divers 2024; 28:61-71. [PMID: 36609739 DOI: 10.1007/s11030-022-10595-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/26/2022] [Indexed: 01/09/2023]
Abstract
An efficient visible light mediated, eosin Y catalyzed direct C-H oxidative amination of benzoxazoles with secondary amines has been developed, which providing a straightforward, green, and environmentally benign access to a wide variety of substituted benzoxazole-2-amines under mild reaction conditions. The biological studies such as drug-likeness and molecular docking are also carried out on the molecule.
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Affiliation(s)
- Mohd Zaheeruddin Beg
- Department of Chemistry, CMP Degree College, University of Allahabad, Prayagraj, 211002, India
| | - Pravin K Singh
- Department of Chemistry, CMP Degree College, University of Allahabad, Prayagraj, 211002, India
| | - Praveen P Singh
- Department of Chemistry, United College of Engineering & Research, Naini, Prayagraj, 211010, India
| | - Manish Srivastava
- Department of Chemistry, University of Allahabad, Prayagraj, 211002, India
| | - Vishal Srivastava
- Department of Chemistry, CMP Degree College, University of Allahabad, Prayagraj, 211002, India.
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36
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Boussaha S, Lassed S, Abdelwahab AB, Krid A, Altun M, Chalard PP, Chalchat PJC, Figueredo G, Zama PD, Demirtas PI, Benayache PS, Benayache PF. Chemical Characterization, DNA-Damage Protection, Antiproliferative Activity and in Silico Studies of the Essential Oils from Perralderia coronopifolia Coss. Chem Biodivers 2024; 21:e202301535. [PMID: 38010960 DOI: 10.1002/cbdv.202301535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/22/2023] [Accepted: 11/26/2023] [Indexed: 11/29/2023]
Abstract
In this study, for the first time, we analyzed the chemical composition of essential oils (EOs) steam-distilled from the flowers and leaves of Perralderia coronopifolia by GC-FID/MS. The objective was to explore new anticancer and antioxidant bioactive substances and understand their mechanisms of action through the use of plant-derived natural products. The major chemical components characterizing the EOs were cis-chrysanthenyl acetate 1, 6-oxocyclonerolidol 2, cis-8-acetoxychrysanthenyl acetate 3, and 6α-hydroxycyclonerolidol 4, respectively. Furthermore, the EOs inhibited cell proliferation in HeLa (human cervix carcinoma) and PC3 (human prostate cancer) cells and protected plasmid DNA from oxidative damage caused by UV-photolyzed H2 O2 . Employing a molecular docking study, we elucidated the main compounds' inhibition mechanisms. Consequently, the antitumor activity could be related to the inhibitory property of compound 3 against CDC25B phosphatase. The evaluation of ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties and the density functional theory (DFT) calculations of the major compounds, especially compound 3, offer potential insights for designing and developing new cancer drug candidates. In conclusion, our study provides a framework for future research and development in the field by establishing a scientific foundation for the use of Perralderia coronopifolia essential oils as a prospective source of antioxidant and anticancer agents.
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Affiliation(s)
- Sara Boussaha
- Unité de Recherche: Valorisation des Ressources Naturelles, Molécules Bioactives et Analyses Physicochimiques et Biologiques, Université Frères Mentouri, Constantine 1. Route d'Aïn El Bey, 25017, Constantine, Algérie
- Higher National School of Biotechnology Taoufik KHAZNADAR, nouveau Pôle universitaire Ali Mendili, BP. E66, Constantine, 25100, Algeria
| | - Somia Lassed
- Département de Microbiologie et Biochimie, Université Mostefa Benboulaid, Batna-2, 05078, Batna, Algérie
| | - Ahmed B Abdelwahab
- Temisis Therapeutics, 19 avenue de la Forêt de Haye, 54500, Vandœuvre-lès-Nancy, France
| | - Adel Krid
- Laboratoire de Physique Mathématique et Subatomique LPMS, Département de Chimie, Université des Frères Mentouri, 25017, Constantine, Algeria
- Pharmaceutical Sciences Research Center (CRSP), Ali Mendjli, Constantine, 25000, Algeria
| | - Muhammed Altun
- Plant research laboratory, Chemistry Department, Cankiri Karatekin University, Ballica Campus, 18100, Cankiri, Turkey
| | - Pr Pierre Chalard
- Université Clermont Auvergne, CNRS SIGMA Clermont ICC, F-63000, Clermont Ferrand, France
| | - Pr Jean Claude Chalchat
- Association de Valorisation des Huiles Essentielles et des Arômes (AVAHEA), La Laye 7, 63500, Saint Babel, France
| | - Gilles Figueredo
- Laboratoire d'Analyses des Extraits Végétaux et des Arômes (LEXVA Analytique), 460 Rue du Montant, 63110, Beaumont, France
| | - Pr Djamila Zama
- Unité de Recherche: Valorisation des Ressources Naturelles, Molécules Bioactives et Analyses Physicochimiques et Biologiques, Université Frères Mentouri, Constantine 1. Route d'Aïn El Bey, 25017, Constantine, Algérie
| | - Pr Ibrahim Demirtas
- Plant research laboratory, Chemistry Department, Cankiri Karatekin University, Ballica Campus, 18100, Cankiri, Turkey
| | - Pr Samir Benayache
- Unité de Recherche: Valorisation des Ressources Naturelles, Molécules Bioactives et Analyses Physicochimiques et Biologiques, Université Frères Mentouri, Constantine 1. Route d'Aïn El Bey, 25017, Constantine, Algérie
| | - Pr Fadila Benayache
- Unité de Recherche: Valorisation des Ressources Naturelles, Molécules Bioactives et Analyses Physicochimiques et Biologiques, Université Frères Mentouri, Constantine 1. Route d'Aïn El Bey, 25017, Constantine, Algérie
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Ćurčić V, Olszewski M, Maciejewska N, Višnjevac A, Srdić-Rajić T, Dobričić V, García-Sosa AT, Kokanov SB, Araškov JB, Silvestri R, Schüle R, Jung M, Nikolić M, Filipović NR. Quinoline-based thiazolyl-hydrazones target cancer cells through autophagy inhibition. Arch Pharm (Weinheim) 2024; 357:e2300426. [PMID: 37991233 DOI: 10.1002/ardp.202300426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
Heterocyclic pharmacophores such as thiazole and quinoline rings have a significant role in medicinal chemistry. They are considered privileged structures since they constitute several Food and Drug Administration (FDA)-approved drugs for cancer treatment. Herein, we report the synthesis, in silico evaluation of the ADMET profiles, and in vitro investigation of the anticancer activity of a series of novel thiazolyl-hydrazones based on the 8-quinoline (1a-c), 2-quinoline (2a-c), and 8-hydroxy-2-quinolyl moiety (3a-c). The panel of several human cancer cell lines and the nontumorigenic human embryonic kidney cell line HEK-293 were used to evaluate the compound-mediated in vitro anticancer activities, leading to [2-(2-(quinolyl-8-ol-2-ylmethylene)hydrazinyl)]-4-(4-methoxyphenyl)-1,3-thiazole (3c) as the most promising compound. The study revealed that 3c blocks the cell-cycle progression of a human colon cancer cell line (HCT-116) in the S phase and induces DNA double-strand breaks. Also, our findings demonstrate that 3c accumulates in lysosomes, ultimately leading to the cell death of the hepatocellular carcinoma cell line (Hep-G2) and HCT-116 cells, by the mechanism of autophagy inhibition.
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Affiliation(s)
- Vladimir Ćurčić
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Mateusz Olszewski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Natalia Maciejewska
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | | | - Tatjana Srdić-Rajić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Vladimir Dobričić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | | | - Sanja B Kokanov
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | | | - Romano Silvestri
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Roland Schüle
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Manfred Jung
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Milan Nikolić
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
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38
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Antonijevic M, Charou D, Davis A, Curel T, Valcarcel M, Ramos I, Villacé P, Claeysen S, Dallemagne P, Gravanis A, Charalampopoulos I, Rochais C. Development of Pleiotropic TrkB and 5-HT 4 Receptor Ligands as Neuroprotective Agents. Molecules 2024; 29:515. [PMID: 38276593 PMCID: PMC10819171 DOI: 10.3390/molecules29020515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
One common event that is the most detrimental in neurodegenerative disorders, even though they have a complex pathogenesis, is the increased rate of neuronal death. Endogenous neurotrophins consist of the major neuroprotective factors, while brain-derived neurotrophic factor (BDNF) and its high-affinity tyrosine kinase receptor TrkB are described in a number of studies for their important neuronal effects. Normal function of this receptor is crucial for neuronal survival, differentiation, and synaptic function. However, studies have shown that besides direct activation, the TrkB receptor can be transactivated via GPCRs. It has been proven that activation of the 5-HT4 receptor and transactivation of the TrkB receptor have a positive influence on neuronal differentiation (total dendritic length, number of primary dendrites, and branching index). Because of that and based on the main structural characteristics of LM22A-4, a known activator of the TrkB receptor, and RS67333, a partial 5-HT4 receptor agonist, we have designed and synthesized a small data set of novel compounds with potential dual activities in order to not only prevent neuronal death, but also to induce neuronal differentiation in neurodegenerative disorders.
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Affiliation(s)
- Mirjana Antonijevic
- Normandie University, Unicaen, Centre d’Etudes et de Recherche sur le Médicament de Normandie (CERMN), 14000 Caen, France; (M.A.); (A.D.); (P.D.)
| | - Despoina Charou
- Department of Pharmacology, Medical School, University of Crete, 70013 Heraklion, Greece; (D.C.); (A.G.); (I.C.)
- Institute of Molecular Biology & Biotechnology, Foundation of Research & Technology-Hellas, 70013 Heraklion, Greece
| | - Audrey Davis
- Normandie University, Unicaen, Centre d’Etudes et de Recherche sur le Médicament de Normandie (CERMN), 14000 Caen, France; (M.A.); (A.D.); (P.D.)
| | - Thomas Curel
- IGF, Univ Montpellier, CNRS, INSERM, 34000 Montpellier, France; (T.C.); (S.C.)
| | | | - Isbaal Ramos
- Innoprot S.L, 48160 Derio, Spain; (M.V.); (I.R.); (P.V.)
| | | | - Sylvie Claeysen
- IGF, Univ Montpellier, CNRS, INSERM, 34000 Montpellier, France; (T.C.); (S.C.)
| | - Patrick Dallemagne
- Normandie University, Unicaen, Centre d’Etudes et de Recherche sur le Médicament de Normandie (CERMN), 14000 Caen, France; (M.A.); (A.D.); (P.D.)
| | - Achille Gravanis
- Department of Pharmacology, Medical School, University of Crete, 70013 Heraklion, Greece; (D.C.); (A.G.); (I.C.)
- Institute of Molecular Biology & Biotechnology, Foundation of Research & Technology-Hellas, 70013 Heraklion, Greece
| | - Ioannis Charalampopoulos
- Department of Pharmacology, Medical School, University of Crete, 70013 Heraklion, Greece; (D.C.); (A.G.); (I.C.)
- Institute of Molecular Biology & Biotechnology, Foundation of Research & Technology-Hellas, 70013 Heraklion, Greece
| | - Christophe Rochais
- Normandie University, Unicaen, Centre d’Etudes et de Recherche sur le Médicament de Normandie (CERMN), 14000 Caen, France; (M.A.); (A.D.); (P.D.)
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39
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Das S, Halder D, Jeyaprakash RS. Computational-guided approach for identification of PI3K alpha inhibitor in the treatment of hepatocellular carcinoma by virtual screening and water map analysis. J Biomol Struct Dyn 2024:1-23. [PMID: 38197431 DOI: 10.1080/07391102.2023.2300131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024]
Abstract
Hepatocellular carcinoma (HCC) is one of the most deadly disorders, with a relative survival rate of 36% in the last 5 years. After an extensive literature survey and pathophysiology analysis, PI3Kα was found to be a promising biological target as PIK3CA gene upregulation was observed in HCC, resulting in the loss of apoptosis of cells, which leads to uncontrollable growth and proliferation. Due to superior selectivity and promising therapeutic activity, the PI3K-targeted molecule library was selected, and the ligand preparation was executed. The study mainly focused on e-pharmacophore development, virtual screening and receptor-ligand docking analysis. Then, MMGBSA and ADME prediction analysis was performed with the top 10 molecules; for further analysis of ligand-receptor binding affinity at the catalytic binding site, induced fit docking was performed with the top two molecules. The analysis of quantum chemical stability descriptors, i.e., frontier molecular orbital analysis, was performed followed by molecular dynamics simulation of 100 ns to better understand the ligand-receptor binding. In this study, water map analysis played a significant role in the hit optimization and analysis of the thermodynamic properties of the receptor-ligand complex. The two hit molecules K894-1435 and K894-1045 represented superior docking scores, enhanced stability, and inhibitory action targeting Valine 851 amino acid residue at the catalytic binding site. Hence, the study has significance for the quest for selective PI3Kα inhibitors through the process of hit-to-lead optimization.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Debojyoti Halder
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - R S Jeyaprakash
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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40
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Azzouzi M, Azougagh O, Ouchaoui AA, El hadad SE, Mazières S, Barkany SE, Abboud M, Oussaid A. Synthesis, Characterizations, and Quantum Chemical Investigations on Imidazo[1,2- a]pyrimidine-Schiff Base Derivative: ( E)-2-Phenyl- N-(thiophen-2-ylmethylene)imidazo[1,2- a]pyrimidin-3-amine. ACS OMEGA 2024; 9:837-857. [PMID: 38222514 PMCID: PMC10785637 DOI: 10.1021/acsomega.3c06841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/17/2023] [Indexed: 01/16/2024]
Abstract
In this study, (E)-2-phenyl-N-(thiophen-2-ylmethylene)imidazo[1,2-a]pyrimidin-3-amine (3) is synthesized, and detailed spectral characterizations using 1H NMR, 13C NMR, mass, and Fourier transform infrared (FT-IR) spectroscopy were performed. The optimized geometry was computed using the density functional theory method at the B3LYP/6-311++G(d,p) basis set. The theoretical FT-IR and NMR (1H and 13C) analysis are agreed to validate the structural assignment made for (3). Frontier molecular orbitals, molecular electrostatic potential, Mulliken atomic charge, electron localization function, localized orbital locator, natural bond orbital, nonlinear optical, Fukui functions, and quantum theory of atoms in molecules analyses are undertaken and meticulously interpreted, providing profound insights into the molecular nature and behaviors. In addition, ADMET and drug-likeness studies were carried out and investigated. Furthermore, molecular docking and molecular dynamics simulations have been studied, indicating that this is an ideal molecule to develop as a potential vascular endothelial growth factor receptor-2 inhibitor.
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Affiliation(s)
- Mohamed Azzouzi
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Omar Azougagh
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Abderrahim Ait Ouchaoui
- Laboratory
of Medical Biotechnology (MedBiotech), Bionova Research Center, Medical
and Pharmacy School, Mohammed V University, Agdal, Rabat B.P 8007, Morocco
| | - Salah eddine El hadad
- Laboratory
of Medical Biotechnology (MedBiotech), Bionova Research Center, Medical
and Pharmacy School, Mohammed V University, Agdal, Rabat B.P 8007, Morocco
| | - Stéphane Mazières
- Laboratory
of IMRCP, University Paul Sabatier, CNRS
UMR 5623, 118 route de Narbonne, Toulouse 31062, France
| | - Soufian El Barkany
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Mohamed Abboud
- Catalysis
Research Group (CRG), Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Adyl Oussaid
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
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41
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Zaky YA, Rashad MW, Zaater MA, El Kerdawy AM. Discovery of dual rho-associated protein kinase 1 (ROCK1)/apoptosis signal-regulating kinase 1 (ASK1) inhibitors as a novel approach for non-alcoholic steatohepatitis (NASH) treatment. BMC Chem 2024; 18:2. [PMID: 38172941 PMCID: PMC10765837 DOI: 10.1186/s13065-023-01081-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
In the current study we suggest a novel approach to curb non-alcoholic steatohepatitis (NASH) progression, and we suggest privileged scaffolds for the design of novel compounds for this aim. NASH is an advanced form of non-alcoholic fatty liver disease that can further progress into fibrosis, cirrhosis, and hepatocellular carcinoma. It is a widely emerging disease affecting 25% of the global population and has no current approved treatments. Protein kinases are key regulators of cellular pathways, of which, Rho-associated protein kinase 1 (ROCK1) and apoptosis signal-regulating kinase 1 (ASK1) play an important role in the progression of NASH and they stand out as promising targets for NASH therapy. Interestingly, their kinase domains are found to be similar in sequence and topology; therefore, dual inhibition of ROCK1 and ASK1 is expected to be amenable and could achieve a more favourable outcome. To reach this goal, a training set of ROCK1 and ASK1 protein structures co-crystalized with type 1 (ATP-competitive) inhibitors was constructed to manually generate receptor-based pharmacophore models representing ROCK1 and ASK1 inhibitors' common pharmacophoric features. The models produced were assessed using a test set of both ROCK1 and ASK1 actives and decoys, and their performance was evaluated using different assessment metrics. The best pharmacophore model obtained, showing a Mathew's correlation coefficient (MCC) of 0.71, was then used to screen the ZINC purchasable database retrieving 6178 hits that were filtered accordingly using several medicinal chemistry and pharmacokinetics filters returning 407 promising compounds. To confirm that these compounds are capable of binding to the target kinases, they were subjected to molecular docking simulations at both protein structures. The results were then assessed individually and filtered, setting the spotlight on various privileged scaffolds that could be exploited as the nucleus for designing novel ROCK1/ASK1 dual inhibitors.
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Affiliation(s)
- Yara A Zaky
- Department of Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt.
| | - Mai W Rashad
- Department of Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Marwa A Zaater
- Master Postgraduate Program, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ahmed M El Kerdawy
- Department of Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- School of Pharmacy, College of Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, Lincolnshire, UK
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42
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Singh L, Kaur H, Chandra Arya G, Bhatti R. Neuroprotective potential of formononetin, a naturally occurring isoflavone phytoestrogen. Chem Biol Drug Des 2024; 103:e14353. [PMID: 37722967 DOI: 10.1111/cbdd.14353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/17/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023]
Abstract
The increased prevalence of neurological illnesses is a burgeoning challenge to the public healthcare system and presents greater financial pressure. Formononetin, an O-methylated isoflavone, has gained a lot of attention due to its neuroprotective potential explored in several investigations. Formononetin is widely found in legumes and several types of clovers including Trifolium pratense L., Astragalus membranaceus, Sophora tomentosa, etc. Formononetin modulates various endogenous mediators to confer neuroprotection. It prevents RAGE activation that results in the inhibition of neuronal damage via downregulating the level of ROS and proinflammatory cytokines. Furthermore, formononetin also increases the expression of ADAM-10, which affects the pathology of neurodegenerative disease by lowering tau phosphorylation, maintaining synaptic plasticity, and boosting hippocampus neurogenesis. Besides these, formononetin also increases the expression of antioxidants, Nrf-2, PI3K, ApoJ, and LRP1. Whereas, reduces the expression of p65-NF-κB and proinflammatory cytokines. It also inhibits the deposition of Aβ and MAO-B activity. An inhibition of Aβ/RAGE-induced activation of MAPK and NOX governs the protection elicited by formononetin against inflammatory and oxidative stress-induced neuronal damage. Besides this, PI3K/Akt and ER-α-mediated activation of ADAM10, ApoJ/LRP1-mediated clearance of Aβ, and MAO-B inhibition-mediated preservation of dopaminergic neurons integrity are the major modulations produced by formononetin. This review covers the biosynthesis of formononetin and key molecular pathways modulated by formononetin to confer neuroprotection.
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Affiliation(s)
- Lovedeep Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
- University Institute of Pharma Sciences, Chandigarh University, Mohali, India
| | - Harpreet Kaur
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | - Girish Chandra Arya
- University Institute of Pharma Sciences, Chandigarh University, Mohali, India
| | - Rajbir Bhatti
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
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43
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Boateng ST, Roy T, Agbo ME, Mahmud MA, Banang-Mbeumi S, Chamcheu RCN, Yadav RK, Bramwell M, Pham LK, Dang DD, Jackson KE, Nagalo BM, Hill RA, Efimova T, Fotie J, Chamcheu JC. Multifaceted approach toward mapping out the anticancer properties of small molecules via in vitro evaluation on melanoma and nonmelanoma skin cancer cells, and in silico target fishing. Chem Biol Drug Des 2024; 103:e14418. [PMID: 38230791 DOI: 10.1111/cbdd.14418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/16/2023] [Accepted: 10/02/2023] [Indexed: 01/18/2024]
Abstract
Melanoma and nonmelanoma skin cancers are among the most prevalent and most lethal forms of skin cancers. To identify new lead compounds with potential anticancer properties for further optimization, in vitro assays combined with in-silico target fishing and docking have been used to identify and further map out the antiproliferative and potential mode of action of molecules from a small library of compounds previously prepared in our laboratory. From screening these compounds in vitro against A375, SK-MEL-28, A431, and SCC-12 skin cancer cell lines, 35 displayed antiproliferative activities at the micromolar level, with the majority being primarily potent against the A431 and SCC-12 squamous carcinoma cell lines. The most active compounds 11 (A431: IC50 = 5.0 μM, SCC-12: IC50 = 2.9 μM, SKMEL-28: IC50 = 4.9 μM, A375: IC50 = 6.7 μM) and 13 (A431: IC50 = 5.0 μM, SCC-12: IC50 = 3.3 μM, SKMEL-28: IC50 = 13.8 μM, A375: IC50 = 17.1 μM), significantly and dose-dependently induced apoptosis of SCC-12 and SK-MEL-28 cells, as evidenced by the suppression of Bcl-2 and upregulation of Bax, cleaved caspase-3, caspase-9, and PARP protein expression levels. Both agents significantly reduced scratch wound healing, colony formation, and expression levels of deregulated cancer molecular targets including RSK/Akt/ERK1/2 and S6K1. In silico target prediction and docking studies using the SwissTargetPrediction web-based tool suggested that CDK8, CLK4, nuclear receptor ROR, tyrosine protein-kinase Fyn/LCK, ROCK1/2, and PARP, all of which are dysregulated in skin cancers, might be prospective targets for the two most active compounds. Further validation of these targets by western blot analyses, revealed that ROCK/Fyn and its associated Hedgehog (Hh) pathways were downregulated or modulated by the two lead compounds. In aggregate, these results provide a strong framework for further validation of the observed activities and the development of a more comprehensive structure-activity relationship through the preparation and biological evaluation of analogs.
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Affiliation(s)
- Samuel T Boateng
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Tithi Roy
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Mercy E Agbo
- Department of Chemistry and Physics, Southeastern Louisiana University, Hammond, Louisiana, USA
| | - Md Ashiq Mahmud
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Sergette Banang-Mbeumi
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Roxane-Cherille N Chamcheu
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Rajesh K Yadav
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Marion Bramwell
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Long K Pham
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Danny D Dang
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Keith E Jackson
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Bolni Marius Nagalo
- Department of Pathology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, USA
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Science (UAMS), Little Rock, Arkansas, USA
| | - Ronald A Hill
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Tatiana Efimova
- Department of Biomedical Engineering, Northwestern University, Chicago, Illinois, USA
| | - Jean Fotie
- Department of Chemistry and Physics, Southeastern Louisiana University, Hammond, Louisiana, USA
| | - Jean Christopher Chamcheu
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
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44
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Dinata R, Nisa N, Arati C, Rasmita B, Uditraj C, Siddhartha R, Bhanushree B, Saeed-Ahmed L, Manikandan B, Bidanchi RM, Abinash G, Pori B, Khushboo M, Roy VK, Gurusubramanian G. Repurposing immune boosting and anti-viral efficacy of Parkia bioactive entities as multi-target directed therapeutic approach for SARS-CoV-2: exploration of lead drugs by drug likeness, molecular docking and molecular dynamics simulation methods. J Biomol Struct Dyn 2024; 42:43-81. [PMID: 37021347 DOI: 10.1080/07391102.2023.2192797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023]
Abstract
The COVID-19 pandemic has caused adverse health (severe respiratory, enteric and systemic infections) and environmental impacts that have threatened public health and the economy worldwide. Drug repurposing and small molecule multi-target directed herbal medicine therapeutic approaches are the most appropriate exploration strategies for SARS-CoV-2 drug discovery. This study identified potential multi-target-directed Parkia bioactive entities against SARS-CoV-2 receptors (S-protein, ACE2, TMPRSS2, RBD/ACE2, RdRp, MPro, and PLPro) using ADMET, drug-likeness, molecular docking (AutoDock, FireDock and HDOCK), molecular dynamics simulation and MM-PBSA tools. One thousand Parkia bioactive entities were screened out by virtual screening and forty-five bioactive phytomolecules were selected based on favorable binding affinity and acceptable pharmacokinetic and pharmacodynamics properties. The binding affinity values of Parkia phyto-ligands (AutoDock: -6.00--10.40 kcal/mol; FireDock: -31.00--62.02 kcal/mol; and HDOCK: -150.0--294.93 kcal/mol) were observed to be higher than the reference antiviral drugs (AutoDock: -5.90--9.10 kcal/mol; FireDock: -35.64--59.35 kcal/mol; and HDOCK: -132.82--211.87 kcal/mol), suggesting a potent modulatory action of Parkia bioactive entities against the SARS-CoV-2. Didymin, rutin, epigallocatechin gallate, epicatechin-3-0-gallate, hyperin, ursolic acid, lupeol, stigmasta-5,24(28)-diene-3-ol, ellagic acid, apigenin, stigmasterol, and campesterol strongly bound with the multiple targets of the SARS-CoV-2 receptors, inhibiting viral entry, attachment, binding, replication, transcription, maturation, packaging and spread. Furthermore, ACE2, TMPRSS2, and MPro receptors possess significant molecular dynamic properties, including stability, compactness, flexibility and total binding energy. Residues GLU-589, and LEU-95 of ACE2, GLN-350, HIS-186, and ASP-257 of TMPRSS2, and GLU-14, MET-49, and GLN-189 of MPro receptors contributed to the formation of hydrogen bonds and binding interactions, playing vital roles in inhibiting the activity of the receptors. Promising results were achieved by developing multi-targeted antiviral Parkia bioactive entities as lead and prospective candidates under a small molecule strategy against SARS-CoV-2 pathogenesis. The antiviral activity of Parkia bioactive entities needs to be further validated by pre-clinical and clinical trials.
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Affiliation(s)
- Roy Dinata
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Nisekhoto Nisa
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Chettri Arati
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Chetia Uditraj
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | | | | | - Bose Manikandan
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Giri Abinash
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Buragohain Pori
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Maurya Khushboo
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Vikas Kumar Roy
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
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Yakan H, Bilir G, Çakmak Ş, Taş Ö, Türköz Karakullukçu N, Soydan E, Kütük H, Güçlü C, Şentürk M, Arslan T, Öztürk S, Aksakal E, Ekinci D. Inhibitory effects of sulfenimides on human and bovine carbonic anhydrase enzymes. J Enzyme Inhib Med Chem 2023; 38:2194573. [PMID: 36971264 PMCID: PMC10044159 DOI: 10.1080/14756366.2023.2194573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
A series of sulfenimide derivatives (1a-i) were investigated as inhibitors of human (hCA-I, hCA-II) and bovine (bCA) carbonic anhydrase enzymes. The compounds were synthesised by the reaction of substituted thiophenols with phthalimide by means of an effective, simple and eco-friendly method and the structures were confirmed by IR, 1H NMR, 13C NMR, MS and elemental analysis. All derivatives except for the methyl derivative (1b) exhibited effective inhibitory action at low micromolar concentrations on human isoforms, but only four derivatives (1e, 1f, 1h, 1i) inhibited the bovine enzyme. The bromo derivative (1f) was found to be strongest inhibitor of all three enzymes with KI values of 0.023, 0.044 and 20.57 µM for hCA-I, hCA-II and bCA, respectively. Results of our study will make valuable contributions to carbonic anhydrase inhibition studies for further investigations since inhibitors of this enzyme are important molecules for medicinal chemistry.
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Yurttaş L, Evren AE, Kubilay A, Aksoy MO, Temel HE, Akalın Çiftçi G. Synthesis of Some New 1,3,4-Oxadiazole Derivatives and Evaluation of Their Anticancer Activity. ACS OMEGA 2023; 8:49311-49326. [PMID: 38162760 PMCID: PMC10753699 DOI: 10.1021/acsomega.3c07776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
In this work, some new 2-[(5-((2-acetamidophenoxy)methyl)-1,3,4-oxadiazol-2-yl)thio]acetamide derivatives (4a-4l) were synthesized and studied for their anticancer activity. Twelve new compounds were tested on the A549 human lung cancer cell line, C6 rat glioma cell line, and L929 murine fibroblast cell line. Compounds 4f, 4i, 4k, and 4l (IC50: 1.59-7.48 μM), and especially 4h (IC50: <0.14 μM), exhibited excellent cytotoxic profile on A549 with selectivity. Compounds 4g and 4h showed remarkable antiproliferative activity on the C6 cell line with IC50 values of 8.16 and 13.04 μM, respectively. The compounds with the lowest IC50 value on the A549 cell line (4f, 4h, 4i, 4k, and 4l) were further studied to determine the mechanism of action. These compounds were found to induce apoptosis with a higher ratio (16.10-21.54%) than that of the standard drug cisplatin (10.07%). Compound 4f displayed mitochondrial membrane depolarization and caspase-3 activation at most, whereas compounds 4h (89.66%) and 4i (78.78%) had outstanding retention rates in the G0/G1phase of the cell cycle (cisplatin 74.75%). Compounds 4f, 4g, 4h, and 4l exhibited matrix metalloproteinase-9 (MMP-9) inhibition higher than 75% at 100 μg/mL; even IC50 values were found to be 1.65 and 2.55 μM for 4h and 4l. In addition, in silico physicochemical properties of the compounds and molecular docking interaction of compound 4h on the MMP-9 enzyme were evaluated; the desired and expected results were obtained.
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Affiliation(s)
- Leyla Yurttaş
- Faculty
of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, 26470 Eskişehir, Turkey
| | - Asaf Evrim Evren
- Faculty
of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, 26470 Eskişehir, Turkey
- Department
of Pharmacy Services, Vocational School of Health Services, Bilecik Şeyh Edebali University, 11000 Bilecik, Turkey
| | - Aslıhan Kubilay
- Faculty
of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, 26470 Eskişehir, Turkey
| | - Mehmet Onur Aksoy
- Faculty
of Pharmacy, Department of Biochemistry, Anadolu University, 26470 Eskişehir, Turkey
| | - Halide Edip Temel
- Faculty
of Pharmacy, Department of Biochemistry, Anadolu University, 26470 Eskişehir, Turkey
| | - Gülşen Akalın Çiftçi
- Faculty
of Pharmacy, Department of Biochemistry, Anadolu University, 26470 Eskişehir, Turkey
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Zhang X, Wang M, Liang X, Wang J, Zhang M, Li C, Wei L, Bi H. Bioinformatics analysis and in vivo validation study of Ophiocordyceps sinensis (Berk.)G.H.Sungetal against lung adenocarcinoma. JOURNAL OF ETHNOPHARMACOLOGY 2023; 317:116739. [PMID: 37315647 DOI: 10.1016/j.jep.2023.116739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/08/2023] [Accepted: 06/04/2023] [Indexed: 06/16/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Lung adenocarcinoma (LUAD) is one of the main types of lung cancer. Ophiocordyceps sinensis has many potentially useful pharmacologic features, such as lung protection, and both anti-inflammatory and antioxidant activities. AIM OF THE STUDY This study was conducted to investigate-using bioinformatics and in vivo experimental validation-the possible role of O. sinensis against LUAD. MATERIALS AND METHODS We obtained important targets of O. sinensis for the treatment of LUAD using network pharmacology techniques and deep mining of the TCGA database, and validated them by molecular docking techniques and in vivo experiments. RESULTS Through bioinformatics analysis and research, we screened BRCA1 and CCNE1 as important biomarkers for LUAD and as core targets of O. sinensis against LUAD. The non-small cell lung cancer signaling pathway, PI3K-Akt signaling pathway, and HIF-1 signaling pathway are potentially important pathways of O. sinensis against LUAD. The molecular docking results showed good binding between the active components in O. sinensis and the two core targets, and the in vivo experimental validation results indicated that O. sinensis had good inhibitory effects in the Lewis lung cancer (LLC) model. CONCLUSIONS BRCA1 and CCNE1 are crucial biomarkers for LUAD and are important targets for O. sinensis to exert anti-LUAD effects.
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Affiliation(s)
- Xingfang Zhang
- Qinghai Provincial Key Laboratory of Tibetan Medicine Pharmacology and Safety Evaluation, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining, 810008, China; Medical College, Qinghai University, Xining, 810001, China.
| | - Mengyuan Wang
- Medical College, Qinghai University, Xining, 810001, China.
| | - Xinxin Liang
- Qinghai Provincial Key Laboratory of Tibetan Medicine Pharmacology and Safety Evaluation, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining, 810008, China.
| | - Jianv Wang
- Qinghai Provincial Key Laboratory of Tibetan Medicine Pharmacology and Safety Evaluation, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining, 810008, China.
| | - Ming Zhang
- Qinghai Provincial Key Laboratory of Tibetan Medicine Pharmacology and Safety Evaluation, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining, 810008, China; CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
| | - Cen Li
- Qinghai Provincial Key Laboratory of Tibetan Medicine Pharmacology and Safety Evaluation, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining, 810008, China; CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
| | - Lixin Wei
- Qinghai Provincial Key Laboratory of Tibetan Medicine Pharmacology and Safety Evaluation, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining, 810008, China; CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
| | - Hongtao Bi
- Qinghai Provincial Key Laboratory of Tibetan Medicine Pharmacology and Safety Evaluation, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining, 810008, China.
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48
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Rocha Caldas G, do Amaral L, Munhoz Rodrigues D, Mayrink de Miranda A, Aparecida Guinaim Dos Santos N, Machado Rocha L, Tame Parreira RL, Cardozo Dos Santos A, Kenupp Bastos J. Brazilian Green Propolis' Artepillin C and Its Acetylated Derivative Activate the NGF-Signaling Pathways and Induce Neurite Outgrowth in NGF-Deprived PC12 Cells. Chem Biodivers 2023; 20:e202301294. [PMID: 37953436 DOI: 10.1002/cbdv.202301294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/14/2023]
Abstract
Artepillin C is the most studied compound in Brazilian Green Propolis and, along with its acetylated derivative, displays neurotrophic activity on PC12 cells. Specific inhibitors of the trkA receptor (K252a), PI3K/Akt (LY294002), and MAPK/ERK (U0126) signaling pathways were used to investigate the neurotrophic mechanism. The expression of proteins involved in axonal and synaptic plasticity (GAP-43 and Synapsin I) was assessed by western blotting. Additionally, physicochemical properties, pharmacokinetics, and drug-likeness were evaluated by the SwissADME web tool. Both compounds induced neurite outgrowth by activating the NGF-signaling pathways but through different neuronal proteins. Furthermore, in silico analyses showed interesting physicochemical and pharmacokinetic properties of these compounds. Therefore, these compounds could play an important role in axonal and synaptic plasticity and should be further investigated.
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Affiliation(s)
- Gabriel Rocha Caldas
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Lilian do Amaral
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Débora Munhoz Rodrigues
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Aline Mayrink de Miranda
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Leandro Machado Rocha
- Natural Products Technology Laboratory-Fluminense Federal University, Niterói, RJ, Brazil
| | | | | | - Jairo Kenupp Bastos
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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49
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Agarwal N, Fatima A, Bhattacharya P, Muthu S, Arora H, Siddiqui N, Javed S. Evaluation of experimental, computational, molecular docking and dynamic simulation of flucytosine. J Biomol Struct Dyn 2023; 41:10430-10449. [PMID: 36562198 DOI: 10.1080/07391102.2022.2159530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Flucytosine (5-fluorocytosine), a fluorine derivative of pyrimidine, has been studied both experimentally and quantum chemically. To obtain the optimized structure, vibrational frequencies and other various parameters, the B3LYP method with a 6-311++G(d,p) basis set was used. Atom-in-molecule theory was used to calculate the binding energies, ellipticity and isosurface projection by electron localization of the molecule (AIM). In addition, the computational results from IR and Raman were compared with the experimental spectra. NBO analysis was used to analyze the donor and acceptor interactions. To know the reactive region of the molecule, the molecular electrostatic potential (MEP) and Fukui functions were determined. The UV-Vis spectrum calculated by the TD-DFT/PCM method was also compared with the experimentally determined spectrum. The HOMO-LUMO energy outcomes proved that there was a good charge exchange occurring within the molecule. With DMSO and MeOH as the solvents, maps of the hole and electron density distribution (EDD and HDD) were produced in an excited state. An electrophilicity index parameter was looked at to theoretically test the bioactivity of the compound. To find the best ligand-protein interactions, molecular docking was also carried out with various receptor proteins. In order to verify the inhibitory potency for the receptor protein complex predicted by docking and molecular dynamic simulation studies, the binding free energy of the receptor protein complex was calculated. Using the MM/GBSA technique, we determined the docked complex's binding free energy. To confirm the molecule's drug similarity, a biological drug similarity investigation was also executed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Agarwal
- Department of chemistry, Institute of H. Science, Dr. Bhimrao-Ambedkar University, Agra, Uttar Pradesh, India
| | - Aysha Fatima
- S.O.S in chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | | | - S Muthu
- Department of Physics, Aringnar Anna Government Arts College, Cheyyar, India
| | - Himanshu Arora
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
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50
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Zaib S, Younas MT, Khan I, Ali HS, McAdam CJ, White JM, Jaber F, Awwad NS, Ibrahium HA. Pyrimidine-morpholine hybrids as potent druggable therapeutics for Alzheimer's disease: Synthesis, biochemical and in silico analyses. Bioorg Chem 2023; 141:106868. [PMID: 37738768 DOI: 10.1016/j.bioorg.2023.106868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/02/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023]
Abstract
The identification of effective and druggable cholinesterase inhibitors to treat progressive neurodegenerative Alzheimer's disorder remains a continuous drug discovery hunt. In this perspective, the present study investigates the design and discovery of pyrimidine-morpholine hybrids (5a-l) as potent cholinesterase inhibitors. Palladium-catalyzed Suzuki-Miyaura cross-coupling reaction was employed to introduce the structural diversity on the pyrimidine heterocyclic core. A range of commercially available boronic acids was successfully coupled showing a high functional group tolerance. In vitro cholinesterase inhibitory potential using Ellman's method revealed significantly strong potency. Compound 5h bearing a meta-tolyl substituent at 2-position of pyrimidine ring emerged as a lead candidate against AChE with an inhibitory potency of 0.43 ± 0.42 µM, ∼38-fold stronger value than neostigmine (IC50 = 16.3 ± 1.12 µM). Compound 5h also showed the lead inhibition against BuChE with an IC50 value of 2.5 ± 0.04 µM. The kinetics analysis of 5h revealed the non-competitive mode of inhibition against AChE whereas computational modelling results of potent leads depicted diverse contacts with the binding site amino acid residues. Molecular dynamics simulations revealed the stability of biomolecular system, while, ADME analysis demonstrated druglikeness behaviour of potent compounds. Overall, the investigated pyrimidine-morpholine scaffold presented a remarkable potential to be developed as efficacious anti-Alzheimer's drugs.
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Affiliation(s)
- Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan.
| | - Muhammad Tayyab Younas
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Imtiaz Khan
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester MI 7DN, UK.
| | - Hafiz Saqib Ali
- Chemistry Research Laboratory, Department of Chemistry and the INEOS Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | | | - Jonathan M White
- School of Chemistry and Bio-21 Institute, University of Melbourne, 3052 Parkville, Australia
| | - Fadi Jaber
- Department of Biomedical Engineering, Ajman University, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Nasser S Awwad
- Department of Chemistry, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hala A Ibrahium
- Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
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